Pro-angiogenic genes in ovarian tumor endothelial cell isolates

ABSTRACT

A gene profiling signature for ovarian tumor endothelial cells is disclosed herein. The gene signature can be used to diagnosis or prognosis an ovarian tumor, identify agents to treat an ovarian tumor, to predict the metastatic potential of an ovarian tumor and to determine the effectiveness of ovarian tumor treatments. Thus, methods are provided for identifying agents that can be used to treat ovarian cancer, for determining the effectiveness of an ovarian tumor treatment, or to diagnose or prognose an ovarian tumor. Methods of treatment are also disclosed which include administering a composition that includes a specific binding agent that specifically binds to one of the disclosed ovarian endothelial cell tumor-associated molecules and inhibits ovarian tumor in the subject.

CROSS REFERENCE TO RELATED APPLICATIONS

This is a divisional of U.S. patent application Ser. No. 12/541,729, filed Aug. 14, 2009, which is a continuation-in-part application of International Patent Application PCT/US2008/054014, filed Feb. 14, 2008, designating the United States and published in English as WO 2008/101118, which claims the benefit of U.S. Provisional Application No. 60/901,455, filed on Feb. 14, 2007. The entire contents of these prior applications are incorporated herein by reference.

ACKNOWLEDGMENT OF GOVERNMENT SUPPORT

This invention was made with government support under contract CA083639 awarded by the National Institutes of Health. The government has certain rights in the invention.

FIELD OF THE DISCLOSURE

This disclosure relates to the field of ovarian cancer and in particular, to methods for treating ovarian cancer by targeting ovarian endothelial cell tumor-associated molecules identified by an ovarian tumor endothelial cell gene expression profile and methods for identifying therapeutic agents.

BACKGROUND

Ovarian cancer is the fifth most common form of cancer in women in the United States, accounting for three percent of the total number of cancer cases and twenty-six percent of those occurring in the female genital tract. The American Cancer Society estimated that 15,310 deaths would be caused in women living in the United States in 2006. A large majority of women who die of ovarian cancer will have had serous carcinoma of the ovarian epithelium, a condition which occurs in sixty percent of all cases of ovarian cancer (Boring et al., Cancer J. Clin. 44: 7-26, 1994).

Women with ovarian cancer are typically asymptomatic until the cancer has metastasized. As a result, most women with ovarian cancer are not diagnosed until the cancer has progressed to an advanced and usually incurable stage (Boente et al., Curr. Probl. Cancer 20: 83-137, 1996). Survival rates are much better in women diagnosed with early-stage ovarian cancers, about ninety percent of these women are still alive five years after diagnosis.

Treatment of ovarian cancer typically involves a variety of treatment modalities. Generally, surgical intervention serves as the basis for treatment (Dennis S. Chi & William J. Hoskins, Primary Surgical Management of Advanced Epithelial Ovarian Cancer, in Ovarian Cancer 241, Stephen C. Rubin & Gregory P. Sutton eds., 2d ed. 2001). Treatment of serous carcinoma often involves cytoreductive surgery (hysterectomy, bilateral salpingo-oophorectomy, omentectomy, and lymphadenectomy) followed by adjuvant chemotherapy with paclitaxel and either cisplatin or carboplatin (Eltabbakh, G. H. & Awtrey, C. S., Expert Op. Pharmacother. 2(10): 109-24, 2001).

Despite a clinical response rate of 80% to primary treatment with surgery and chemotherapy, most subjects experience tumor recurrence within two years of treatment. The overwhelming majority of subjects will eventually develop chemoresistance and die as a result of their cancer. Thus, a need exists to identify alternative treatments for ovarian cancer.

SUMMARY OF THE DISCLOSURE

A gene profiling signature is disclosed herein that can be used to predict clinical outcome and develop therapeutics for treating ovarian cancer in a subject. For example, the ovarian endothelial cell tumor-associated molecules identified by the gene profile signature can serve as prognostic indicators as well as targets for specific therapeutic molecules that can reduce or eliminate ovarian cancer. Thus, methods of identifying an agent for treating an ovarian tumor are provided. In some examples, the methods include contacting a cell, such as an ovarian tumor cell or an ovarian tumor endothelial cell, with one or more test agents under conditions sufficient for the one or more test agents to alter the activity of at least one ovarian endothelial cell tumor-associated molecule listed in any of Tables 1-5. The method includes detecting the activity of the at least one ovarian endothelial cell tumor-associated molecule in the presence and absence of the one or more test agents. The activity of the at least one ovarian endothelial cell tumor-associated molecule in the presence of the one or more test agents is then compared to the activity in the absence of such agents to determine if there is differential expression of the at least one ovarian endothelial cell tumor associated molecule. Differential expression of the ovarian endothelial cell tumor-associated molecule in the presence of the test agent(s) indicates that the one or more test agents can be used to treat an ovarian tumor.

Methods are also provided for treating an ovarian tumor. In some examples, the method includes administering to the subject a therapeutically effective treatment to inhibit ovarian tumor growth. In an example, the treatment includes administering a therapeutically effective amount of a specific binding agent that binds with high specificity to one of the ovarian endothelial cell tumor-associated molecules listed in Tables 1, 2, 4 or 5 and alters expression or activity of the molecules, thereby treating the ovarian tumor in the subject (for example, by decreasing tumor vascular growth, tumor growth or tumor volume). In particular examples, the specific binding agent preferentially binds to and inhibits expression or activity of one of the ovarian endothelial cell tumor-associated molecules that is upregulated in an ovarian tumor endothelial cell, such as Zeste homologue 2 (EZH2), EGF-like domain, multiple 6 (EGFL6), tumor necrosis factor, alpha-induced protein 6 (TNFAIP6), Twist homologue 1 (TWIST1), stanniocalcin 1 (STC1), homeodomain-only protein (HOP), chondroitin sulfate proteoglycan 2 (CSPG2), and plexin domain containing 1 (PLXDC1). In other particular examples, ovarian tumor growth is inhibited by the specific binding agent preferentially binding to and inhibiting expression of one of the ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4 or 5 which are involved in angiogenesis, such as molecules involved in cell proliferation, tube formation or cell motility and are upregulated in ovarian tumor endothelial cells.

Methods are also provided for determining the effectiveness of an agent for the treatment of an ovarian tumor in a subject with the ovarian tumor. In an example, the method includes detecting expression of an ovarian endothelial cell tumor-associated molecule in a sample from the subject following administration of the agent. The expression of the ovarian endothelial cell tumor-associated molecule following administration is compared to a control, such as specific binding agents that bind to and inhibit one of the ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4 or 5 that is upregulated in ovarian endothelial tumor cells. An alteration in the expression of the ovarian endothelial cell tumor-associated molecule (such as a decrease in expression of a molecule upregulated in ovarian tumor endothelial cells or an increase in expression of a molecule downregulated in such cells) following treatment indicates that the agent is effective for the treatment of the ovarian cancer in the subject. In a specific example, the method includes detecting and comparing the protein expression levels of the ovarian endothelial cell tumor-associated molecules. In other examples, the method includes detecting and comparing the mRNA expression levels of the ovarian endothelial cell tumor-associated molecules.

Methods of diagnosing and prognosing an ovarian tumor (such as a tumor that overexpresses at least one of the disclosed ovarian endothelial cell tumor-associated molecules) are provided. In some examples, such methods are performed prior to the treatment methods described herein. However, such methods can also be used independently of the disclosed treatment methods. In particular examples, the method includes determining the metastatic potential of an ovarian tumor in a subject by detecting expression of at least one ovarian endothelial cell tumor-associated molecule in a sample obtained from a subject with an ovarian tumor. The at least one ovarian endothelial cell tumor-associated molecule is involved in promoting angiogenesis, such as cell proliferation, cell motility or tube formation, such as EZH2. The method further includes comparing expression of the at least one ovarian endothelial cell tumor-associated molecule in the sample obtained from the subject with the ovarian tumor to a control. An alteration in the expression of the at least one ovarian endothelial cell tumor-associated molecule involved in promoting angiogenesis indicates that the subject has an ovarian tumor with increased metastatic potential.

In additional examples, methods are disclosed for predicting a clinical outcome in a subject with an ovarian tumor, such as advanced stage epithelial ovarian cancer. In an example, the methods include detecting expression of at least one ovarian endothelial cell tumor-associated molecules listed in Tables 1-5 or combinations thereof (such as at least 1, at least 3, at least 5 or at least 10 of such molecules) in a sample obtained from the subject with the ovarian tumor. The methods also can include comparing expression of the at least one ovarian endothelial cell tumor-associated molecule in the sample obtained from the subject with the ovarian tumor to a control (such as a normal sample or value representing such expression expected in a normal sample), wherein an alteration in the expression of the at least one ovarian endothelial cell tumor-associated molecule indicates that the subject has a decreased chance of survival. For example, an alteration in the expression, such as an increase in the expression of EZH2 indicates a poor prognosis, such as a decreased chance of survival. In one example, a decreased chance of survival includes a survival time of equal to or less than a year. Alterations in the expression can be measured using methods known in the art, and this disclosure is not limited to particular methods. For example, expression can be measured at the nucleic acid level (such as by real time quantitative polymerase chain reaction or microarray analysis) or at the protein level (such as by Western blot analysis).

The foregoing and other features of the disclosure will become more apparent from the following detailed description of several embodiments which proceeds with reference to the accompanying figures.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a graph illustrating the comparative fold change in relative expression levels between microarray data and real-time quantitative RT-PCR data of selected genes from the pro-angiogenic gene signature provided in Table 1.

FIG. 2 is a graph illustrating protein expression in ovarian endothelial cells for a subset of the proteins detected following staining of samples with immunofluorescently-labeled PTK2, Fyn, MMP-9, β2-arrestin, Jagged1 and PLXDC1.

FIGS. 3A, 3B and 3C are digital images of siRNA-mediated silencing of (FIG. 3A) EZH2, (FIG. 3B) Jagged1 and (FIG. 3C) protein tyrosine kinase 2 (PTK2), as assessed using Western blot analyses.

FIG. 3D is a graph illustrating the effect of EZH2, Jagged1 or PTK2 silencing on human umbilical vein endothelial cell (HUVEC) tube formation.

FIG. 3E is a graph illustrating the effect of EZH2 silencing on HUVEC migration.

FIG. 3F is a graph illustrating the effect of Jagged1 silencing on HUVEC migration.

FIG. 3G is a graph illustrating the effect of PTK2 silencing on HUVEC migration.

FIG. 4 is a digital image illustrating down regulation of EZH2 by mouse EZH2 siRNA in mouse ovarian endothelial cells.

FIGS. 5A, 5B and 6 provide graphs illustrating the therapeutic effects of siRNA-mediated EZH2 down regulation on HeyA8 (FIG. 5A) and SKOV3ip1 (FIGS. 5B and 6) ovarian tumors.

FIGS. 7A-7H illustrate EZH2 expression in human ovarian carcinoma. FIG. 7A provides digital images representative of human tumors with low and high EZH2 expression based on immunohistochemical staining FIG. 7B provides Kaplan-Meier curves of disease-specific mortality for patients whose ovarian tumors expressed high and low levels of EZH2 (EZH2-T). The log-rank test (two-sided) was used to compare differences between the two groups. Increased EZH2-T was significantly associated with decreased overall survival (p<0.001). FIG. 7C provides digital images representative of human ovarian tumor vasculature (arrowheads point to endothelial cells) with low and high immunohistochemical staining for EZH2. FIG. 7D provides Kaplan-Meier curves of disease-specific mortality of patients whose ovarian vasculature expressed low versus high EZH2 (EZH2-Endo). EZH2-Endo was predictive of poor overall survival. FIG. 7E provides digital images representative of human ovarian tumors with low or high immunohistochemical staining for VEGF. FIG. 7F provides a bar graph VEGF expression was strongly associated with high EZH2-Endo (*p<0.01). FIG. 7G provides digital images representative of human ovarian tumors with low or high immunohistochemical staining for microvessel density (MVD). FIG. 7H provides a bar graph illustrating high MVD counts in a tumor were significantly associated with high EZH2-Endo expression (*p<0.001). Images in panels A, C, and E were taken at original magnification ×200, and in panel g at original magnification ×200.

FIGS. 8A-8C are graphs illustrating VEGF-increased EZH2 expression in endothelial cells. Results in FIGS. 8A and 8B are in response to 6-hour treatments with EGF (25 ng/μL), VEGF (50 ng/μL), conditioned medium (CM) from the non-cancerous ovarian epithelial cell line IOSE120, two ovarian cancer cell lines OVCA420 and SKOV3, and complete medium with either 10% serum (A) or 2% serum (B). Percent fold changes represent the mean+/−s.d. of triplicate experiments compared to untreated control cells. *p<0.05; **p<0.01; ***p<0.001. FIG. 8A illustrates that EZH2 promoter activity is increased in an endothelial cell line in response to EGF, VEGF, and conditioned media from ovarian cancer cell lines. EAhy926 hybridoma endothelial cell line was cotransfected with the Renilla luciferase plasmid and firefly luciferase plasmid either with or without the EZH2 promoter construct followed by treatment with EGF, VEGF and conditioned medium and promoter activity was determined. FIG. 8B illustrates that EZH2 mRNA levels are increased in HUVEC in response to EGF, VEGF, and conditioned media from ovarian cancer cell lines. Cells were treated as indicated and purified RNA was used in real-time quantitative RT-PCR. Control values were normalized using 3 housekeeping genes. FIG. 8C Pearson's analysis shows significant correlation between EZH2 and VEGF expression values (Log₂) from 29 microdissected high-grade serous papillary ovarian adenocarcinomas.

FIGS. 9A-9E show EZH2 gene silencing increases VASH1 mRNA expression in endothelial cells. FIG. 9A is a digital image of a polyacrylamide gel illustrating PCR products generated by as ChIP assay of EZH2 binding to human VASH1 promoter in response to VEGF in HUVEC. Cross-linked chromatin from HUVEC was treated with (+) or without (−) VEGF and immunoprecipitated (IP) using EZH2 or mouse IgG antibodies. The input and immunoprecipitated DNA were subjected to PCR using primers corresponding to the 3800 to 3584 base pairs upstream of VASH1 transcription start site. PCR products were examined on ethidium bromide-stained agarose gel. FIG. 9B is a bar graph illustrating EZH2 mRNA levels in cells transfected with control or mouse EZH2 siRNA and harvested after 72 hours. RNA was isolated and subjected to real-time quantitative RT-PCR. The fold difference in levels of EZH2 mRNA represents the mean of triplicate experiments compared to control siRNA treated cells. Error bars represent s.e.m. *p<0.05. FIG. 9C is a bar graph illustrating the fold difference in levels of VASH1 mRNA as compared to control siRNA treated cells. Error bars represent s.e.m. *p<0.01. FIG. 9D illustrates the effect of EZH2 gene silencing on methylation status of VASH1 in VEGF-treated MOECs as detected by methylation specific PCR. The inhibitory units of methylated VASH1 were normalized by that of the un-methylated VASH1 and represent the mean of triplicate experiments. FIG. 9E is a digital image of a Western blot of lysate collected 48 hours after transfection of MOEC with control, VEGF treated and mouse EZH2 siRNA treated cells.

FIGS. 10A-10C show E2F transcription factors increases upon VEGF treatment in MOEC. FIG. 10A is a bar graph illustrating expression levels of E2F transcription factors in MOEC. Cells were treated with VEGF for 6 hours and subjected to Q-RT-PCR. FIG. 10B provides a pair of bar graphs illustrating silencing of E2F1, E2F3 and E2F5 transcription factors by targeted siRNA in MOEC. Cells were transfected with corresponding siRNAs. After 24 hours and 48 hours, cells were collected; RNA was isolated and was subjected to real-time Q-RT-PCR. E2F3 and E2F5 gene silencing decreases EZH2 expression levels. EZH2 expression levels were analyzed in E2F1, E2F3 and E2F5 silenced samples using Q-RT-PCR. The fold difference in levels of mRNA expression represents the mean of triplicate experiments compared to cells (A) and VEGF treated cells (B). Error bars represent s.e.m. *p<0.01. FIG. 10C is a bar graph illustrating the effect of VASH1 gene silencing on tube formation in endothelial cells. HUVECs were plated on Matrigel after transfecting the cells with either control or human VASH1 siRNA. Vascular tube formation was evaluated by microscopic observation.

FIGS. 11A-11E illustrate the physical characteristics of siRNA/CH nanoparticles. FIG. 11A is a table providing the composition of CH/TPP/siRNAs. FIG. 11B is a graph illustrating the mean particle size of siRNA/CH particles as measured using light scattering with a particle analyzer, showing that nanoparticles maintained 100-200 nm size up to 7:1 ratio (CH:TPP). FIG. 11C is a graph illustrating that zeta potential of siRNA/CH nanoparticles showed slight positive charge. FIG. 11D is a graph illustrating incorporation efficiency of siRNA into CH nanoparticles with 3:1 ratio of CH:TPP resulting in >75% incorporation efficiency. FIG. 11E is a digital image following atomic force microscopy (AFM) demonstrating that siRNA/CH nanoparticles were spherical and <150 nm in size.

FIGS. 12A-12E illustrate incorporation, stability and intracellular uptake of siRNA/CH nanoparticles. FIG. 12A is a digital image illustrating electrophoretic migration of naked siRNA and siRNA/CH nanoparticles. SiRNA/CH nanoparticles (open arrow) remained at top of the gel compared to naked siRNA (solid arrow), which migrated downward. FIG. 12B is a digital image illustrating electrophoretic migration of siRNA/CH nanoparticles in the presence of 50% serum. SiRNA/CH nanoparticles were collected at different time points of incubation at 37° C. (Lane 1; naked siRNA, Lanes 2 to 5; siRNA/CH nanoparticles). Naked siRNA (solid arrow) was degraded over 12 to 24 hours in serum containing media; whereas CH nanoparticles (open arrow) protected the siRNA from degradation in serum. Increased binding efficiency of siRNA/CH nanoparticles was noted compared to naked siRNA. FIG. 12C is a fluorescence microscopy digital image of HeyA8 cells after incubating either with siRNA alone or with siRNA/CH nanoparticles at 4° C. for 20 minutes in PBS. FIG. 12D is a series of tracings from a flow cytometry analysis demonstrating that uptake efficiency of nanoparticles into cells was increased by 72-fold after incubating cells in PBS at 4° C. for 20 minutes. FIG. 12E is graphical representation of percentage of uptake of Alexa-555 siRNA by cells by flow cytometry analysis.

FIGS. 13A-13E illustrate in vivo siRNA delivery using CH nanoparticles and the distribution of siRNA following single intravenous injection of Alexa-555 siRNA/CH nanoparticles in orthotopic HeyA8 tumor bearing nude mice. FIG. 13A provides a pair of digital images illustrating fluorescent siRNA distribution in tumor tissue of hematoxylin and eosin, original magnification ×200 (left); stained with anti-CD31 (green) antibody to detect endothelial cells (right). FIG. 13B provides a pair of digital images of 50-μm sections stained with Cytox Green and examined with confocal microscopy (original magnification ×400) (left); lateral view (right). Images taken every 1 μm were stacked and examined from the lateral view. Nuclei were labeled green and fluorescent siRNA (red) was seen throughout the section. At all time points, punctated emissions of the siRNA were noted in the perinuclear regions of individual cells, and siRNA was seen in >80% of fields examined. (c) Western blot of lysates from orthotopic tumors collected 24, 48, 72 and 96 hours after a single injection of control siRNA/CH or human (EZH2 Hs siRNA/CH). FIG. 13D provides multiple digital images illustrating EZH2 gene silencing in HeyA8 tumor as well as tumor endothelial cells. Tumors were collected after 48 hours of single injection of control siRNA/CH, or EZH2 Hs siRNA/CH, or EZH2 Mm siRNA/CH and stained for EZH2 (green) and CD31 (red). Images were taken at original magnification, ×200. FIG. 13E is a pair of graphs illustrating the effects of EZH2 Hs siRNA/CH or EZH2 Mm siRNA/CH on tumor weight in mouse orthotopic tumor models. Nude mice were injected with HeyA8 or SKOV3ip 1 ovarian cancer cells and 1 week later, were randomly assigned (10 mice per group) to receive therapy: (1) control siRNA/CH, (2) EZH2 Hs siRNA/CH, (3) EZH2 Mm siRNA/CH, and (4) combination of EZH2 Hs siRNA/CH plus EZH2 Mm siRNA/CH. Mice were sacrificed when any animals in control or a treatment group became moribund (after 3 to 4 weeks of therapy) and mouse weight, tumor weight and tumor location were recorded. Error bars represent s.e.m. *p<0.05; **p<0.001.

FIG. 14 provides a series of digital images of Western blots of lysate collected 72 hours after transfection of HeyA8 cells or MOEC with control, human EZH2, or mouse EZH2 siRNA.

FIG. 15 is a pair of graphs illustrating the weight distribution of HeyA8 and SKOV3ip1 tumors. Seven days following tumor cell injection, mice were randomly divided into 4 groups (10 mice per group) to receive therapy: (1) control siRNA/CH, (2) EZH2 Hs siRNA/CH, (3) EZH2 Mm siRNA/CH, and (4) combination of EZH2 Hs siRNA/CH plus EZH2 Mm siRNA/CH. Mice were sacrificed when any animals in control or a treatment group became moribund (after 3 to 4 weeks of therapy) and tumor weight was recorded.

FIGS. 16A-16B (A) Effect of tumor (EZH2 Hs siRNA/CH) or endothelial (EZH2 Mm siRNA/CH) targeted EZH2 siRNA on MVD and pericyte coverage. Tumors harvested following 3 to 4 weeks of therapy were stained for CD31 (MVD; red) and desmin (pericyte coverage; green). All pictures were taken at original magnification ×200. The bars in the graphs correspond sequentially to the labeled columns of images at left. Error bars represent s.e.m. *p<0.05; **p<0.001. (B) Effects of VASH1 gene silencing on tumor growth in vivo. Nude mice were injected with SKOV3ip1 ovarian cancer cells and 1 week later, were randomly divided into 5 groups (10 mice per group): (1) control siRNA/CH, (2) EZH2 Mm siRNA1/CH, (3) EZH2 Mm siRNA2/CH (4) EZH2 Mm siRNA3/CH (5) VASH1 Mm siRNA1/CH and (6) combination of EZH2 Mm siRNA1/CH plus VASH1 Mm siRNA/CH. FIG. 16B is a bar graph illustrating the number of cells that migrated in the presence and absence of VASH1 siRNA. Mice were sacrificed when any animals in control or a treatment group became moribund (after 3 to 4 weeks of therapy) and mouse weight, tumor weight and tumor location were recorded. Error bars represent s.e.m. *p<0.05.

FIG. 17 illustrates the effects of EZH2 Hs siRNA/CH or EZH2 Mm siRNA/CH on proliferation. Tumors were harvested following 3-4 weeks of therapy and then stained for proliferating cell nuclear antigen (PCNA). All images were taken at original magnification ×100. The bars in the graphs correspond sequentially to the labeled columns of images at left. Error bars represent s.e.m. *p<0.05.

SEQUENCE LISTING

The nucleic and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. In the accompanying sequence listing:

SEQ ID NOS: 1, 6-27, and 44-47 are nucleic acid sequences of exemplary primers.

SEQ ID NOS: 2-5 and 28-43 are nucleic acid sequences of exemplary siRNAs.

DETAILED DESCRIPTION OF SEVERAL EMBODIMENTS

Despite improvements in surgery and chemotherapy, mortality rates in women with advanced ovarian carcinoma have remained largely unchanged (Cannistra, N. Engl. J. Med. 329: 1550-1559, 1993). Therefore, novel therapeutic strategies are needed. Growth of tumors, both at the primary and metastatic sites, requires a blood supply for expansion beyond 1-2 mm (Folkman, J. Nat. Canc. Inst. 82: 4-6, 1990). Targeting tumor angiogenesis by inhibiting endothelial cells that support tumor growth is particularly promising because of their presumed genetic stability. The recent success of a humanized monoclonal antibody bevacizumab (trade name Avastin®) against vascular endothelial growth factor in prolonging the lives of patients with advanced colon and breast carcinoma demonstrates the promise of such approaches (Hurwitz et al., N. Engl. J. Med. 350: 2335-2342, 2004 and Jain et al., Nat. Clin. Pract. Oncol. 3: 24-40, 2006). However, the full spectrum of differences in the tumor vasculature compared to its normal counterpart is not known. Identification of additional targets on tumor endothelium may allow opportunities for developing new therapeutic approaches to inhibit angiogenesis in a tumor-specific manner.

In recent years, whole genome expression profiling of cancer using methods such as microarray and serial analysis of gene expression (SAGE) have provided insight into the molecular pathways involved in cancer onset and progression. While selected genes in ovarian cancer vasculature have been characterized, there is little information regarding global gene expression alterations in ovarian cancer endothelium.

Disclosed herein is a gene expression signature identifying endothelial cell tumor-associated molecules in ovarian tumor endothelial cell isolates. Endothelial cells were purified from human ovarian tissues and invasive ovarian epithelial cancers, and a gene expression profile was established for ovarian tumor endothelial cells using microarray analyses. The gene expression profile disclosed herein identifies genes whose expression is differentially regulated in tumor versus normal endothelial cells. This profile reveals distinct expression profiles for tumor endothelial cell isolates as compared to non-tumor endothelial isolates.

The disclosed gene expression profile also reveals genes and collections or sets of genes that serve as effective molecular markers for angiogenesis in ovarian cancer, predict clinical outcome as well as such genes or gene sets that can provide clinically effective therapeutic targets for ovarian cancer. This has significant implications for the treatment of ovarian cancer. For example, methods are disclosed for treating ovarian cancer (for example, reducing or inhibiting ovarian cancer growth by targeting ovarian endothelial cell tumor-associated molecules, such as molecules believed to be involved in angiogenesis). For example, molecules involved in cell motility, tube formation or cell proliferation can be identified by the gene profile signature. In an example, a therapeutically effective amount of a specific binding agent is administered to a subject. For example, the specific binding agent preferentially binds to one or more of the identified ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4, 5 or a combination thereof to alter the expression or activity of such molecule (e.g., increase expression or activity of a molecule that is downregulated in ovarian endothelial tumor cells or decrease expression or activity of a molecule that is upregulated in such cells). In one example, the specific binding agent preferentially binds to one or more of the identified ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4, 5 or a combination thereof that are upregulated in ovarian endothelial tumor cells (as indicated by a positive fold change in Table 1) to decrease expression or activity of the one or more molecules. As a result, ovarian cancer in the subject is thereby reduced or eliminated. In a particular example, the specific binding agent is an inhibitor, such as a siRNA, of one or more of the disclosed ovarian endothelial cell tumor-associated molecules described in any of Table 1, 2, 4 or 5 whose expression is upregulated in ovarian endothelial tumor cells, such as EZH2. In some examples, the specific binding agent preferentially binds to one or more of the identified ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4, 5 or a combination thereof that are downregulated in ovarian endothelial tumor cells (as indicated by a negative fold change in Table 1) to increase expression or activity of the one or more molecules. As a result, ovarian cancer in the subject is thereby reduced or eliminated.

TERMS

The following explanations of terms and methods are provided to better describe the present disclosure and to guide those of ordinary skill in the art in the practice of the present disclosure. The singular forms “a,” “an,” and “the” refer to one or more than one, unless the context clearly dictates otherwise. For example, the term “comprising a nucleic acid molecule” includes single or plural nucleic acid molecules and is considered equivalent to the phrase “comprising at least one nucleic acid molecule.” The term “or” refers to a single element of stated alternative elements or a combination of two or more elements, unless the context clearly indicates otherwise. As used herein, “comprises” means “includes.” Thus, “comprising A or B,” means “including A, B, or A and B,” without excluding additional elements.

Unless explained otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this disclosure belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, suitable methods and materials are described below. The materials, methods, and examples are illustrative only and not intended to be limiting.

Administration: To provide or give a subject an agent, such as a chemotherapeutic agent, by any effective route. Exemplary routes of administration include, but are not limited to, injection (such as subcutaneous, intramuscular, intradermal, intraperitoneal, and intravenous), oral, sublingual, rectal, transdermal, intranasal, vaginal and inhalation routes.

Agent: Any protein, nucleic acid molecule, compound, small molecule, organic compound, inorganic compound, or other molecule of interest. Agent can include a therapeutic agent, a diagnostic agent or a pharmaceutical agent. A therapeutic or pharmaceutical agent is one that alone or together with an additional compound induces the desired response (such as inducing a therapeutic or prophylactic effect when administered to a subject). In a particular example, a pharmaceutical agent (such as a siRNA to any of the genes listed in Tables 2 and Table 4) significantly reduces angiogenesis. A test agent is any substance, including, but not limited to, a protein (such as an antibody), nucleic acid molecule (such as a siRNA), organic compound, inorganic compound, or other molecule of interest. In particular examples, a test agent can permeate a cell membrane (alone or in the presence of a carrier).

Amplifying a nucleic acid molecule: To increase the number of copies of a nucleic acid molecule, such as a gene or fragment of a gene, for example a region of an ovarian endothelial cell tumor-associated gene. The resulting products are called amplification products.

An example of in vitro amplification is the polymerase chain reaction (PCR), in which a biological sample obtained from a subject (such as a sample containing ovarian cancer cells) is contacted with a pair of oligonucleotide primers, under conditions that allow for hybridization of the primers to a nucleic acid molecule in the sample. The primers are extended under suitable conditions, dissociated from the template, and then re-annealed, extended, and dissociated to amplify the number of copies of the nucleic acid molecule. Other examples of in vitro amplification techniques include quantitative real-time PCR, strand displacement amplification (see U.S. Pat. No. 5,744,311); transcription-free isothermal amplification (see U.S. Pat. No. 6,033,881); repair chain reaction amplification (see WO 90/01069); ligase chain reaction amplification (see EP-A-320 308); gap filling ligase chain reaction amplification (see U.S. Pat. No. 5,427,930); coupled ligase detection and PCR (see U.S. Pat. No. 6,027,889); and NASBA™ RNA transcription-free amplification (see U.S. Pat. No. 6,025,134).

A commonly used method for real-time quantitative polymerase chain reaction involves the use of a double stranded DNA dye (such as SYBR Green I dye). For example, as the amount of PCR product increases, more SYBR Green I dye binds to DNA, resulting in a steady increase in fluorescence. Another commonly used method is real-time quantitative TaqMan PCR (Applied Biosystems). The 5′ nuclease assay provides a real-time method for detecting only specific amplification products. The use of fluorogenic probes makes it possible to eliminate post-PCR processing for the analysis of probe degradation. The probe is an oligonucleotide with both a reporter fluorescent dye and a quencher dye attached. While the probe is intact, the proximity of the quencher greatly reduces the fluorescence emitted by the reporter dye by Förster resonance energy transfer (FRET) through space. Probe design and synthesis has been simplified by the finding that adequate quenching is observed for probes with the reporter at the 5′ end and the quencher at the 3′ end.

Angiogenesis: A physiological process involving the growth of new blood vessels from pre-existing vessels. Angiogenesis can occur under normal physiological conditions such as during growth and development or wound healing (known as physiological angiogenesis) as well as pathological conditions such as in the transition of tumors from a dormant state to a malignant state (known as pathological angiogenesis). As used herein, pro-angiogenic genes are genes that facilitate angiogenesis, such as angiogenesis in an ovarian tumor.

The complex phenomenon of angiogenesis begins with degradation of the basement membrane by cellular proteases. This allows endothelial cells to penetrate and migrate (process known as cell motility) into the extracellular matrix and then proliferate. In the final stages of this process, the endothelial cells align themselves to form capillary or tubelike structures (process known as tube formation). These new structures then form a network that undergoes significant remodeling and rearrangement before fully functioning capillaries exist. Therefore, angiogenesis can be studied or identified by monitoring tube formation, cell motility, and/or cell proliferation.

Antibody: A polypeptide ligand including at least a light chain or heavy chain immunoglobulin variable region which specifically recognizes and binds an epitope of an antigen, such as an ovarian endothelial cell tumor-associated molecule or a fragment thereof. Antibodies are composed of a heavy and a light chain, each of which has a variable region, termed the variable heavy (V_(H)) region and the variable light (V_(L)) region. Together, the V_(H) region and the V_(L) region are responsible for binding the antigen recognized by the antibody. In one example, an antibody specifically binds to one of the proteins listed in Tables 8 and 9.

This includes intact immunoglobulins and the variants and portions of them well known in the art, such as Fab′ fragments, F(ab)′₂ fragments, single chain Fv proteins (“scFv”), and disulfide stabilized Fv proteins (“dsFv”). A scFv protein is a fusion protein in which a light chain variable region of an immunoglobulin and a heavy chain variable region of an immunoglobulin are bound by a linker, while in dsFvs, the chains have been mutated to introduce a disulfide bond to stabilize the association of the chains. The term also includes genetically engineered forms such as chimeric antibodies (for example, humanized murine antibodies), heteroconjugate antibodies (such as, bispecific antibodies). See also, Pierce Catalog and Handbook, 1994-1995 (Pierce Chemical Co., Rockford, Ill.); Kuby, J., Immunology, 3^(rd) Ed., W.H. Freeman & Co., New York, 1997.

Typically, a naturally occurring immunoglobulin has heavy (H) chains and light (L) chains interconnected by disulfide bonds. There are two types of light chain, lambda and kappa. There are five main heavy chain classes (or isotypes) which determine the functional activity of an antibody molecule: IgM, IgD, IgG, IgA and IgE.

Each heavy and light chain contains a constant region and a variable region, (the regions are also known as “domains”). In combination, the heavy and the light chain variable regions specifically bind the antigen. Light and heavy chain variable regions contain a “framework” region interrupted by three hypervariable regions, also called “complementarity-determining regions” or “CDRs”. The extent of the framework region and CDRs have been defined (see, Kabat et al., Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, 1991, which is hereby incorporated by reference). The Kabat database is now maintained online. The sequences of the framework regions of different light or heavy chains are relatively conserved within a species. The framework region of an antibody, that is the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRs in three-dimensional space.

The CDRs are primarily responsible for binding to an epitope of an antigen. The CDRs of each chain are typically referred to as CDR1, CDR2, and CDR3, numbered sequentially starting from the N-terminus, and are also typically identified by the chain in which the particular CDR is located. Thus, a V_(H) CDR3 is located in the variable domain of the heavy chain of the antibody in which it is found, whereas a V_(L) CDR1 is the CDR1 from the variable domain of the light chain of the antibody in which it is found. An antibody that binds RET will have a specific V_(H) region and the V_(L) region sequence, and thus specific CDR sequences. Antibodies with different specificities (such as different combining sites for different antigens) have different CDRs. Although it is the CDRs that vary from antibody to antibody, only a limited number of amino acid positions within the CDRs are directly involved in antigen binding. These positions within the CDRs are called specificity determining residues (SDRs).

References to “V_(H)” or “VH” refer to the variable region of an immunoglobulin heavy chain, including that of an Fv, scFv, dsFv or Fab. References to “V_(L)” or “VL” refer to the variable region of an immunoglobulin light chain, including that of an Fv, scFv, dsFv or Fab.

A “monoclonal antibody” is an antibody produced by a single clone of B-lymphocytes or by a cell into which the light and heavy chain genes of a single antibody have been transfected. Monoclonal antibodies are produced by methods known to those of skill in the art, for instance by making hybrid antibody-forming cells from a fusion of myeloma cells with immune spleen cells. Monoclonal antibodies include humanized monoclonal antibodies.

A “polyclonal antibody” is an antibody that is derived from different B-cell lines. Polyclonal antibodies are a mixture of immunoglobulin molecules secreted against a specific antigen, each recognizing a different epitope. These antibodies are produced by methods known to those of skill in the art, for instance, by injection of an antigen into a suitable mammal (such as a mouse, rabbit or goat) that induces the B-lymphocytes to produce IgG immunoglobulins specific for the antigen which are then purified from the mammal's serum.

A “chimeric antibody” has framework residues from one species, such as human, and CDRs (which generally confer antigen binding) from another species, such as a murine antibody that specifically binds an ovarian endothelial cell tumor-associated molecule.

A “humanized” immunoglobulin is an immunoglobulin including a human framework region and one or more CDRs from a non-human (for example a mouse, rat, or synthetic) immunoglobulin. The non-human immunoglobulin providing the CDRs is termed a “donor,” and the human immunoglobulin providing the framework is termed an “acceptor.” In one embodiment, all the CDRs are from the donor immunoglobulin in a humanized immunoglobulin. Constant regions need not be present, but if they are, they must be substantially identical to human immunoglobulin constant regions, e.g., at least about 85-90%, such as about 95% or more identical. Hence, all parts of a humanized immunoglobulin, except possibly the CDRs, are substantially identical to corresponding parts of natural human immunoglobulin sequences. Humanized immunoglobulins can be constructed by means of genetic engineering (see for example, U.S. Pat. No. 5,585,089).

Array: An arrangement of molecules, such as biological macromolecules (such as peptides or nucleic acid molecules) or biological samples (such as tissue sections), in addressable locations on or in a substrate. A “microarray” is an array that is miniaturized so as to require or be aided by microscopic examination for evaluation or analysis.

The array of molecules (“features”) makes it possible to carry out a very large number of analyses on a sample at one time. In certain example arrays, one or more molecules (such as an oligonucleotide probe) will occur on the array a plurality of times (such as twice), for instance to provide internal controls. The number of addressable locations on the array can vary, for example from at least one, to at least 2, to at least 5, to at least 10, at least 20, at least 30, at least 50, at least 75, at least 100, at least 150, at least 200, at least 300, at least 500, least 550, at least 600, at least 800, at least 1000, at least 10,000, or more. In particular examples, an array includes nucleic acid molecules, such as oligonucleotide sequences that are at least 15 nucleotides in length, such as about 15-40 nucleotides in length. In particular examples, an array includes oligonucleotide probes or primers which can be used to detect sensitive to ovarian endothelial cell tumor-associated molecule sequences, such as at least one of those listed in Table 1, such as at least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, or at least 1100 sequences listed in Table 1 (for example, 2, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 120, 130, 140, 150, 175, 225, 275, 325, 350, 375, 450, 550, 650, 750, 850, 950, 1050 or 1149 of those listed). In an example, the array is a commercially available such as a U133 Plus 2.0 oligonucleotide array from Affymetrix (Affymetrix, Santa Clara, Calif.).

Within an array, each arrayed sample is addressable, in that its location can be reliably and consistently determined within at least two dimensions of the array. The feature application location on an array can assume different shapes. For example, the array can be regular (such as arranged in uniform rows and columns) or irregular. Thus, in ordered arrays the location of each sample is assigned to the sample at the time when it is applied to the array, and a key may be provided in order to correlate each location with the appropriate target or feature position. Often, ordered arrays are arranged in a symmetrical grid pattern, but samples could be arranged in other patterns (such as in radially distributed lines, spiral lines, or ordered clusters). Addressable arrays usually are computer readable, in that a computer can be programmed to correlate a particular address on the array with information about the sample at that position (such as hybridization or binding data, including for instance signal intensity). In some examples of computer readable formats, the individual features in the array are arranged regularly, for instance in a Cartesian grid pattern, which can be correlated to address information by a computer.

Protein-based arrays include probe molecules that are or include proteins, or where the target molecules are or include proteins, and arrays including nucleic acids to which proteins are bound, or vice versa. In some examples, an array contains antibodies to ovarian endothelial cell tumor-associated proteins, such as any combination of those listed in Table 1, such as at least 2, least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, or at least 1100 sequences listed in Table 1 (for example, 2, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 120, 130, 140, 150, 175, 225, 275, 325, 350, 375, 450, 550, 650, 750, 850, 950, 1050 or 1149 of those listed).

Binding or stable binding: An association between two substances or molecules, such as the hybridization of one nucleic acid molecule to another (or itself), the association of an antibody with a peptide, or the association of a protein with another protein or nucleic acid molecule. An oligonucleotide molecule binds or stably binds to a target nucleic acid molecule if a sufficient amount of the oligonucleotide molecule forms base pairs or is hybridized to its target nucleic acid molecule, to permit detection of that binding. “Preferentially binds” indicates that one molecule binds to another with high affinity, and binds to heterologous molecules at a low affinity.

Binding can be detected by any procedure known to one skilled in the art, such as by physical or functional properties of a target:oligonucleotide complex or a protein:antibody complex. For example, binding can be detected functionally by determining whether binding has an observable effect upon a biosynthetic process such as expression of a gene, DNA replication, transcription, translation, and the like.

Physical methods of detecting the binding of complementary strands of nucleic acid molecules, include but are not limited to, such methods as DNase I or chemical footprinting, gel shift and affinity cleavage assays, Northern blotting, dot blotting and light absorption detection procedures. For example, one method involves observing a change in light absorption of a solution containing an oligonucleotide (or an analog) and a target nucleic acid at 220 to 300 nm as the temperature is slowly increased. If the oligonucleotide or analog has bound to its target, there is a sudden increase in absorption at a characteristic temperature as the oligonucleotide (or analog) and target disassociate from each other, or melt. In another example, the method involves detecting a signal, such as a detectable label, present on one or both nucleic acid molecules (or antibody or protein as appropriate).

The binding between an oligomer and its target nucleic acid is frequently characterized by the temperature (T_(m)) at which 50% of the oligomer is melted from its target. A higher (T_(m)) means a stronger or more stable complex relative to a complex with a lower (T_(m)).

Biological activity: An expression describing the beneficial or adverse effects of an agent on living matter. When the agent is a complex chemical mixture, this activity is exerted by the substance's active ingredient or pharmacophore, but can be modified by the other constituents. Activity is generally dosage-dependent and it is not uncommon to have effects ranging from beneficial to adverse for one substance when going from low to high doses. In one example, a specific binding agent significantly reduces the biological activity of the one or more ovarian endothelial cell tumor-associated molecules that is upregulated in ovarian endothelial tumor cells (such as those listed in Tables 2 and 4) which reduces or eliminates ovarian cancer, such as by reducing or inhibiting angiogenesis. In some examples, a specific binding agent significantly increase the biological activity of one or more ovarian endothelial cell tumor-associated molecules that is downregulated in ovarian endothelial tumor cells (such as those listed in Table 3).

Cancer: The “pathology” of cancer includes all phenomena that compromise the well-being of the subject. This includes, without limitation, abnormal or uncontrollable cell growth, metastasis, interference with the normal functioning of neighboring cells, release of cytokines or other secretory products at abnormal levels, suppression or aggravation of inflammatory or immunological response, neoplasia, premalignancy, malignancy, invasion of surrounding or distant tissues or organs, such as lymph nodes, etc. “Metastatic disease” refers to cancer cells that have left the original tumor site and migrate to other parts of the body for example via the bloodstream or lymph system.

Chemotherapeutic agent or Chemotherapy: Any chemical agent with therapeutic usefulness in the treatment of diseases characterized by abnormal cell growth. Such diseases include tumors, neoplasms, and cancer as well as diseases characterized by hyperplastic growth such as psoriasis. In one embodiment, a chemotherapeutic agent is an agent of use in treating ovarian cancer, such as papillary serous ovarian cancer. In one example, a chemotherapeutic agent is a radioactive compound. One of skill in the art can readily identify a chemotherapeutic agent of use (see for example, Slapak and Kufe, Principles of Cancer Therapy, Chapter 86 in Harrison's Principles of Internal Medicine, 14th edition; Perry et al., Chemotherapy, Ch. 17 in Abeloff, Clinical Oncology 2nd ed., 2000 Churchill Livingstone, Inc; Baltzer and Berkery. (eds): Oncology Pocket Guide to Chemotherapy, 2nd ed. St. Louis, Mosby-Year Book, 1995; Fischer Knobf, and Durivage (eds): The Cancer Chemotherapy Handbook, 4th ed. St. Louis, Mosby-Year Book, 1993). Chemotherapeutic agents used for treating ovarian cancer include, but are not limited to, carboplatin, cisplatin, paclitaxel, docetaxel, doxorubicin, epirubicin, topotecan, irinotecan, gemcitabine, iazofurine, gemcitabine, etoposide, vinorelbine, tamoxifen, valspodar, cyclophosphamide, methotrexate, fluorouracil, mitoxantrone and vinorelbine. Combination chemotherapy is the administration of more than one agent (such as more than one chemotherapeutic agent) to treat cancer.

Chrondroitin sulfate proteoglycan 2 (CSPG2): An extracellular matrix component of the vitreous gel that has been reported to be an anti-cell adhesive. In particular examples, expression of CSPG2 is increased in ovarian cancer endothelial cells. The term CSPG2 includes any CSPG2 gene, cDNA, mRNA, or protein from any organism and that is CSPG2 and is expressed and in some examples overexpressed in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for CSPG2 are publicly available. For example, GenBank Accession Nos.: NM_(—)004385 and BC096495 disclose CSPG2 nucleic acid sequences, and GenBank Accession Nos.: AAH50524, NP_(—)004376, and AAH96495 disclose CSPG2 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, CSPG2 includes a full-length wild-type (or native) sequence, as well as CSPG2 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, CSPG2 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No. AAH50524, NP_(—)004376, or AAH96495. In other examples, CSPG2 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 204619_s_at and 221731_x_a and retains CSPG2 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Complementarity and percentage complementarity: Molecules with complementary nucleic acids form a stable duplex or triplex when the strands bind, (hybridize), to each other by forming Watson-Crick, Hoogsteen or reverse Hoogsteen base pairs. Stable binding occurs when an oligonucleotide molecule remains detectably bound to a target nucleic acid sequence (such as an ovarian endothelial cell tumor-associated molecule) under the required conditions.

Complementarity is the degree to which bases in one nucleic acid strand base pair with the bases in a second nucleic acid strand. Complementarity is conveniently described by percentage, that is, the proportion of nucleotides that form base pairs between two strands or within a specific region or domain of two strands. For example, if 10 nucleotides of a 15-nucleotide oligonucleotide form base pairs with a targeted region of a DNA molecule, that oligonucleotide is said to have 66.67% complementarity to the region of DNA targeted.

In the present disclosure, “sufficient complementarity” means that a sufficient number of base pairs exist between an oligonucleotide molecule and a target nucleic acid sequence (such as a ovarian endothelial cell tumor-associated molecule, for example any of the genes listed in Table 1) to achieve detectable binding. When expressed or measured by percentage of base pairs formed, the percentage complementarity that fulfills this goal can range from as little as about 50% complementarity to full (100%) complementary. In general, sufficient complementarity is at least about 50%, for example at least about 75% complementarity, at least about 90% complementarity, at least about 95% complementarity, at least about 98% complementarity, or even at least about 100% complementarity.

A thorough treatment of the qualitative and quantitative considerations involved in establishing binding conditions that allow one skilled in the art to design appropriate oligonucleotides for use under the desired conditions is provided by Beltz et al. Methods Enzymol. 100:266-285, 1983, and by Sambrook et al. (ed.), Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.

Contacting: Placement in direct physical association, including both a solid and liquid form. Contacting can occur in vitro, for example, with isolated cells or in vivo by administering to a subject.

Decrease: To reduce the quality, amount, or strength of something. In one example, a therapy decreases a tumor (such as the size of a tumor, the growth of a tumor, number of tumors, the metastasis of a tumor, or combinations thereof), or one or more symptoms associated with a tumor, for example as compared to the response in the absence of the therapy (such as a therapy administered to affect tumor size by inhibiting angiogenesis via administration of a binding agent capable of binding to one or more of the ovarian endothelial cell tumor-associated markers listed in Tables 1 through 5 that is involved in promoting angiogenesis, such as by inhibiting an ovarian endothelial cell tumor-associated marker that is upregulated in ovarian endothelial tumor cells or by increasing activity of an ovarian endothelial cell tumor-associated marker that is downregulated in ovarian endothelial tumor cells). In a particular example, a therapy decreases the size of a tumor, the growth of a tumor, the number of tumors, the metastasis of a tumor, or combinations thereof, subsequent to the therapy, such as a decrease of at least 10%, at least 20%, at least 50%, or even at least 90%. Such decreases can be measured using the methods disclosed herein.

Determining expression of a gene product: Detection of a level expression in either a qualitative or quantitative manner.

Diagnosis: The process of identifying a disease by its signs, symptoms and results of various tests. The conclusion reached through that process is also called “a diagnosis.” Forms of testing commonly performed include blood tests, medical imaging, urinalysis, and biopsy.

DNA (deoxyribonucleic acid): A long chain polymer which includes the genetic material of most living organisms (some viruses have genes including ribonucleic acid, RNA). The repeating units in DNA polymers are four different nucleotides, each of which includes one of the four bases, adenine, guanine, cytosine and thymine bound to a deoxyribose sugar to which a phosphate group is attached. Triplets of nucleotides, referred to as codons, in DNA molecules code for amino acid in a polypeptide. The term codon is also used for the corresponding (and complementary) sequences of three nucleotides in the mRNA into which the DNA sequence is transcribed.

Differential expression: A difference, such as an increase or decrease, in the conversion of the information encoded in a gene (such as an ovarian endothelial cell tumor-associated molecule) into messenger RNA, the conversion of mRNA to a protein, or both. In some examples, the difference is relative to a control or reference value, such as an amount of gene expression that is expected in a subject who does not have ovarian cancer or in a normal (non-cancerous) endothelial cell sample. Detecting differential expression can include measuring a change in gene expression.

Downregulated or inactivation: When used in reference to the expression of a nucleic acid molecule, such as a gene, refers to any process which results in a decrease in production of a gene product. A gene product can be RNA (such as mRNA, rRNA, tRNA, and structural RNA) or protein. Therefore, gene downregulation or deactivation includes processes that decrease transcription of a gene or translation of mRNA. Examples of genes whose expression is downregulated in ovarian tumor endothelial cells can be found in Table 1 (indicated by a negative fold change, such as TLOC1 and HS6ST2) and Table 3 (such as PLN, SELE, GREB1, OGN and LCXD3).

Examples of processes that decrease transcription include those that facilitate degradation of a transcription initiation complex, those that decrease transcription initiation rate, those that decrease transcription elongation rate, those that decrease processivity of transcription and those that increase transcriptional repression. Gene downregulation can include reduction of expression above an existing level. Examples of processes that decrease translation include those that decrease translational initiation, those that decrease translational elongation and those that decrease mRNA stability.

Gene downregulation includes any detectable decrease in the production of a gene product. In certain examples, production of a gene product decreases by at least 2-fold, for example at least 3-fold or at least 4-fold, as compared to a control (such an amount of gene expression in a normal endothelial cell). In one example, a control is a relative amount of gene expression or protein expression in a biological sample taken from a subject who does not have ovarian cancer.

Endothelial cell: Cells that line the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall. For example, endothelial cells line the entire circulatory system. Further, both blood and lymphatic capillaries are composed of a single layer of endothelial cells.

Epidermal Growth Factor-like domain multiple 6 (EGFL6): A member of the epidermal growth factor (EGF) repeat superfamily of genes known to encode proteins that govern cellular proliferative responses. EGFL6 has been identified as a possible regulator of cell cycle and oncogenesis.

In particular examples, expression of EGFL6 is increased in ovarian cancer endothelial cells. The term EGFL6 includes any EGFL6 gene, cDNA, mRNA, or protein from any organism and that is EGFL6 and is expressed and in some examples overexpressed in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for EGFL6 are publicly available. For example, GenBank Accession Nos.: NM_(—)015507, NM_(—)019397 and BC038587 disclose EGFL6 nucleic acid sequences, and GenBank Accession Nos.: AAQ88699, CAM23572, and AAF27812 disclose EGFL6 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, EGFL6 includes a full-length wild-type (or native) sequence, as well as EGFL6 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, EGFL6 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No. AAQ88699, CAM23572, or AAF27812. In other examples, EGFL6 has a sequence that hybridizes to Affymetrix Probe ID No. 219454_at and retains EGFL6 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Expression: The process by which the coded information of a gene is converted into an operational, non-operational, or structural part of a cell, such as the synthesis of a protein. Gene expression can be influenced by external signals. For instance, exposure of a cell to a hormone may stimulate expression of a hormone-induced gene. Different types of cells can respond differently to an identical signal. Expression of a gene also can be regulated anywhere in the pathway from DNA to RNA to protein. Regulation can include controls on transcription, translation, RNA transport and processing, degradation of intermediary molecules such as mRNA, or through activation, inactivation, compartmentalization or degradation of specific protein molecules after they are produced.

The expression of a nucleic acid molecule can be altered relative to a normal (wild type) nucleic acid molecule. Alterations in gene expression, such as differential expression, include but are not limited to: (1) overexpression; (2) underexpression; or (3) suppression of expression. Alternations in the expression of a nucleic acid molecule can be associated with, and in fact cause, a change in expression of the corresponding protein. Specific examples of ovarian endothelial cell tumor-associated molecules that are up-regulated in ovarian tumor endothelial cells are provided in Tables 2 and 4. Specific examples of ovarian endothelial cell tumor-associated molecules that are down-regulated in ovarian tumor endothelial cells are listed in Table 3. For example, EZH2, EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, and PLXDC1 are upregulated or increased in expression in ovarian tumor endothelial cells, while TLOC1 and HS6ST2 are downregulated or decreased in expression in such cells.

Protein expression can also be altered in some manner to be different from the expression of the protein in a normal (wild type) situation. This includes but is not necessarily limited to: (1) a mutation in the protein such that one or more of the amino acid residues is different; (2) a short deletion or addition of one or a few (such as no more than 10-20) amino acid residues to the sequence of the protein; (3) a longer deletion or addition of amino acid residues (such as at least 20 residues), such that an entire protein domain or sub-domain is removed or added; (4) expression of an increased amount of the protein compared to a control or standard amount; (5) expression of a decreased amount of the protein compared to a control or standard amount; (6) alteration of the subcellular localization or targeting of the protein; (7) alteration of the temporally regulated expression of the protein (such that the protein is expressed when it normally would not be, or alternatively is not expressed when it normally would be); (8) alteration in stability of a protein through increased longevity in the time that the protein remains localized in a cell; and (9) alteration of the localized (such as organ or tissue specific or subcellular localization) expression of the protein (such that the protein is not expressed where it would normally be expressed or is expressed where it normally would not be expressed), each compared to a control or standard.

Controls or standards for comparison to a sample, for the determination of differential expression, include samples believed to be normal (in that they are not altered for the desired characteristic, for example a sample from a subject who does not have cancer, such as ovarian cancer) as well as laboratory values, even though possibly arbitrarily set, keeping in mind that such values can vary from laboratory to laboratory.

Laboratory standards and values may be set based on a known or determined population value and can be supplied in the format of a graph or table that permits comparison of measured, experimentally determined values.

Gene expression profile (or fingerprint): Differential or altered gene expression can be detected by changes in the detectable amount of gene expression (such as cDNA or mRNA) or by changes in the detectable amount of proteins expressed by those genes. A distinct or identifiable pattern of gene expression, for instance a pattern of high and low expression of a defined set of genes or gene-indicative nucleic acids such as ESTs; in some examples, as few as one or two genes provides a profile, but more genes can be used in a profile, for example at least 3, at least 4, at least 5, at least 6, at least 10, at least 20, at least 25, at least 30, at least 50, at least 80, at least 100, at least 190, at least 200, at least 300, at least 400, at least 500, at least 550, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 1100 or more of those listed in any of Tables 1-5. A gene expression profile (also referred to as a fingerprint) can be linked to a tissue or cell type (such as ovarian cancer cell), to a particular stage of normal tissue growth or disease progression (such as advanced ovarian cancer), or to any other distinct or identifiable condition that influences gene expression in a predictable way. Gene expression profiles can include relative as well as absolute expression levels of specific genes, and can be viewed in the context of a test sample compared to a baseline or control sample profile (such as a sample from a subject who does not have ovarian cancer or normal endothelial cells). In one example, a gene expression profile in a subject is read on an array (such as a nucleic acid or protein array). For example, a gene expression profile is performed using a commercially available array such as a Human Genome U133 2.0 Plus Microarray from AFFYMETRIX® (AFFYMETRIX®, Santa Clara, Calif.).

Homeodomain-only protein, transcript variant 2 (HOP): A transcriptional repressor that modulates serum response factor-dependent cardiac-specific gene expression and cardiac development. In particular examples, expression of HOP is increased in ovarian cancer endothelial cells. The term HOP includes any HOP gene, cDNA, mRNA, or protein from any organism and that is HOP and is expressed and in some examples overexpressed in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for HOP are publicly available. For example, GenBank Accession Nos.: NM_(—)139211, XM_(—)001083738, and XM_(—)001137349 disclose HOP nucleic acid sequences, and GenBank Accession Nos.: AAH14225, NP_(—)631958, and NP_(—)631957 disclose HOP protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, HOP includes a full-length wild-type (or native) sequence, as well as HOP allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, HOP has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: AAH14225, NP_(—)631958, or NP_(—)631957. In other examples, HOP has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 211597_s_at and retains HOP activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Hybridization: To form base pairs between complementary regions of two strands of DNA, RNA, or between DNA and RNA, thereby forming a duplex molecule. Hybridization conditions resulting in particular degrees of stringency will vary depending upon the nature of the hybridization method and the composition and length of the hybridizing nucleic acid sequences. Generally, the temperature of hybridization and the ionic strength (such as the Na⁺ concentration) of the hybridization buffer will determine the stringency of hybridization. Calculations regarding hybridization conditions for attaining particular degrees of stringency are discussed in Sambrook et al., (1989) Molecular Cloning, second edition, Cold Spring Harbor Laboratory, Plainview, N.Y. (chapters 9 and 11). The following is an exemplary set of hybridization conditions and is not limiting:

Very High Stringency (Detects Sequences that Share at Least 90% Identity)

Hybridization: 5×SSC at 65° C. for 16 hours

Wash twice: 2×SSC at room temperature (RT) for 15 minutes each

Wash twice: 0.5×SSC at 65° C. for 20 minutes each

High Stringency (Detects Sequences that Share at Least 80% Identity)

Hybridization: 5×-6×SSC at 65° C.-70° C. for 16-20 hours

Wash twice: 2×SSC at RT for 5-20 minutes each

Wash twice: 1×SSC at 55° C.-70° C. for 30 minutes each

Low Stringency (Detects Sequences that Share Greater than 50% Identity)

Hybridization: 6×SSC at RT to 55° C. for 16-20 hours

Wash at least twice: 2×-3×SSC at RT to 55° C. for 20-30 minutes each.

Inhibitor: Any chemical compound, nucleic acid molecule, peptide or polypeptide such as an antibody or RNAi that can reduce activity of a gene product or interfere with expression of a gene, respectively. In some examples, an inhibitor can reduce or inhibit the activity of a protein that is encoded by a gene either directly or indirectly. Direct inhibition can be accomplished, for example, by binding to a protein and thereby preventing the protein from binding an intended target, such as a receptor. Indirect inhibition can be accomplished, for example, by binding to a protein's intended target, such as a receptor or binding partner, thereby blocking or reducing activity of the protein. In some examples, an inhibitor of the disclosure can inhibit a gene by reducing or inhibiting expression of the gene, inter alia by interfering with gene expression (transcription, processing, translation, post-translational modification), for example, by interfering with the gene's mRNA and blocking translation of the gene product or by post-translational modification of a gene product, or by causing changes in intracellular localization.

Isolated: An “isolated” biological component (such as a nucleic acid molecule, protein, or cell) has been substantially separated or purified away from other biological components in the cell of the organism, or the organism itself, in which the component naturally occurs, such as other chromosomal and extra-chromosomal DNA and RNA, proteins and cells. Nucleic acid molecules and proteins that have been “isolated” include nucleic acid molecules and proteins purified by standard purification methods. The term also embraces nucleic acid molecules and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acid molecules and proteins. For example, an isolated serous papillary ovarian cancer cell is one that is substantially separated from other ovarian cell subtypes, such as endometrioid, clear cell or mucinous subtypes.

Label: An agent capable of detection, for example by ELISA, spectrophotometry, flow cytometry, or microscopy. For example, a label can be attached to a nucleic acid molecule or protein, thereby permitting detection of the nucleic acid molecule or protein. Examples of labels include, but are not limited to, radioactive isotopes, enzyme substrates, co-factors, ligands, chemiluminescent agents, fluorophores, haptens, enzymes, and combinations thereof. Methods for labeling and guidance in the choice of labels appropriate for various purposes are discussed for example in Sambrook et al. (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y., 1989) and Ausubel et al. (In Current Protocols in Molecular Biology, John Wiley & Sons, New York, 1998). In a particular example, a label is conjugated to a binding agent that specifically binds to one or more of the ovarian endothelial cell tumor-associated molecules disclosed in Tables 1 through 5 to allow for the detection/screening for angiogenesis and/or the presence of a tumor in a subject.

Malignant: Cells that have the properties of anaplasia invasion and metastasis.

Mammal: This term includes both human and non-human mammals. Examples of mammals include, but are not limited to: humans and veterinary and laboratory animals, such as pigs, cows, goats, cats, dogs, rabbits and mice.

Neoplasm: Abnormal growth of cells.

Normal Cell: Non-tumor cell, non-malignant, uninfected cell.

Nucleic acid array: An arrangement of nucleic acids (such as DNA or RNA) in assigned locations on a matrix, such as that found in cDNA arrays, or oligonucleotide arrays, such as those listed in Tables 1-5.

Nucleic acid molecules representing genes: Any nucleic acid, for example DNA (intron or exon or both), cDNA, or RNA (such as mRNA), of any length suitable for use as a probe or other indicator molecule, and that is informative about the corresponding gene.

Nucleic acid molecules: A deoxyribonucleotide or ribonucleotide polymer including, without limitation, cDNA, mRNA, genomic DNA, and synthetic (such as chemically synthesized) DNA. The nucleic acid molecule can be double-stranded or single-stranded. Where single-stranded, the nucleic acid molecule can be the sense strand or the antisense strand. In addition, nucleic acid molecule can be circular or linear.

The disclosure includes isolated nucleic acid molecules that include specified lengths of an ovarian endothelial cell tumor-associated molecule nucleotide sequence, for sequences for genes listed in Tables 1 through 4. Such molecules can include at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45 or at least 50 consecutive nucleotides of these sequences or more, and can be obtained from any region of a ovarian endothelial cell tumor-associated molecule.

Oligonucleotide: A plurality of joined nucleotides joined by native phosphodiester bonds, between about 6 and about 300 nucleotides in length. An oligonucleotide analog refers to moieties that function similarly to oligonucleotides but have non-naturally occurring portions. For example, oligonucleotide analogs can contain non-naturally occurring portions, such as altered sugar moieties or inter-sugar linkages, such as a phosphorothioate oligodeoxynucleotide.

Particular oligonucleotides and oligonucleotide analogs can include linear sequences up to about 200 nucleotides in length, for example a sequence (such as DNA or RNA) that is at least 6 nucleotides, for example at least 8, at least 10, at least 15, at least 20, at least 21, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 100 or even at least 200 nucleotides long, or from about 6 to about 50 nucleotides, for example about 10-25 nucleotides, such as 12, 15 or 20 nucleotides.

Oligonucleotide probe: A short sequence of nucleotides, such as at least 8, at least 10, at least 15, at least 20, at least 21, at least 25, or at least 30 nucleotides in length, used to detect the presence of a complementary sequence by molecular hybridization. In particular examples, oligonucleotide probes include a label that permits detection of oligonucleotide probe:target sequence hybridization complexes, such as with an ovarian endothelial cell tumor-associated molecule listed in Tables 1-5.

Ovarian cancer: A malignant ovarian neoplasm (an abnormal growth located on the ovaries). Cancer of the ovaries includes ovarian carcinoma, papillary serous cystadenocarcinoma, mucinous cystadenocarcinoma, endometrioid tumors, celioblastoma, clear cell carcinoma, unclassified carcinoma, granulosa-thecal cell tumors, Sertoli-Leydig cell tumors, dysgerminoma, and malignant teratoma. The most common type of ovarian cancer is papillary serous carcinoma.

Surgery is an exemplary treatment for ovarian cancer and can be necessary for diagnosis. The type of surgery depends upon how widespread the cancer is when diagnosed (the cancer stage), as well as the type and grade of cancer. The surgeon may remove one (unilateral oophorectomy) or both ovaries (bilateral oophorectomy), the fallopian tubes (salpingectomy), and the uterus (hysterectomy). For some very early tumors (stage 1, low grade or low-risk disease), only the involved ovary and fallopian tube will be removed (called a “unilateral salpingo-oophorectomy,” USO), especially in young females who wish to preserve their fertility. In advanced disease as much tumor as possible is removed (debulking surgery). In cases where this type of surgery is successful, the prognosis is improved compared to subjects where large tumor masses (more than 1 cm in diameter) are left behind.

Chemotherapy is often used after surgery to treat any residual disease. At present systemic chemotherapy often includes a platinum derivative with a taxane as a method of treating advanced ovarian cancer. Chemotherapy is also used to treat subjects who have a recurrence.

Ovarian endothelial cell tumor-associated (or related) molecule: A molecule whose expression is altered in ovarian tumor endothelial cells. Such molecules include, for instance, nucleic acid sequences (such as DNA, cDNA, or mRNAs) and proteins. Specific genes include those listed in Tables 1 through 5. Thus, the presence of the respective ovarian endothelial cell tumor-associated molecules can be used to diagnose, or determine the prognosis of, an ovarian tumor in a subject.

In an example, an ovarian endothelial cell tumor-associated molecule is any molecule listed in Tables 1 through 5. Specific examples of ovarian endothelial cell tumor-associated molecules that are up-regulated in ovarian tumor endothelial cells are provided in Tables 2 and 4. Specific examples of ovarian endothelial cell tumor-associated molecules that are down-regulated in ovarian tumor endothelial cells are listed in Table 3. As illustrated in Table 4, a number of the identified ovarian cell tumor-associated molecules are related to cell proliferation, tube formation and cell motility.

Ovarian endothelial cell tumor-associated molecules can be involved in or influenced by cancer in different ways, including causative (in that a change in a ovarian endothelial cell tumor-associated molecule leads to development of or progression of ovarian cancer) or resultive (in that development of or progression of ovarian cancer causes or results in a change in the ovarian endothelial cell tumor-associated molecule).

Pharmaceutically Acceptable Carriers: The pharmaceutically acceptable carriers (vehicles) useful in this disclosure are conventional. Remington's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, Pa., 15th Edition (1975), describes compositions and formulations suitable for pharmaceutical delivery of one or more therapeutic agents, such as one or more compositions that include a binding agent that specifically binds to at least one of the disclosed ovarian endothelial cell tumor-associated molecules.

In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations can include injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. In addition to biologically-neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate, sodium lactate, potassium chloride, calcium chloride, and triethanolamine oleate.

Plexin domain containing 1 (PLXDC1): A large transmembrane receptor. In vitro, plexin-C1 has been shown to bind the GPI-anchored semaphorin Sema7A and the soluble viral semaphorins SemaVA (A39R) and SemaVB (AHV). Plexin C1 engagement by SemaVA inhibits integrin-mediated dendritic cell adhesion and chemotaxis in vitro, suggesting a role for plexin C1 in dendritic cell migration.

In an example, expression of PLXDL1 is increased in ovarian tumor endothelial cells. The term PLXDC1 includes any plexin C1 gene, cDNA, mRNA, or protein from any organism and that is a PLXDC1 and is expressed and in some examples overexpressed in ovarian tumor endothelial cells.

Exemplary nucleic acid and protein sequences for PLXDC1 are publicly available. For example, GenBank Accession Nos.: NM_(—)018797, XM_(—)622776, AB208934, and NM_(—)005761 disclose PLXDC1 nucleic acid sequences and GenBank Accession Nos.: NP_(—)061267, XP_(—)622776, BAD92171, and NP_(—)005752 disclose PLXDC1 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, a PLXDC1 sequence includes a full-length wild-type (or native) sequence, as well as PLXDC1 allelic variants, fragments, homologs or fusion sequences that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, PLXDC1 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: NP_(—)061267, XP_(—)622776, BAD92171, or NP_(—)005752. In other examples, a PLXDC1 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 214081_at and retains PLXDC1 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Polymerase Chain Reaction (PCR): An in vitro amplification technique that increases the number of copies of a nucleic acid molecule (for example, a nucleic acid molecule in a sample or specimen). In an example, a biological sample collected from a subject (e.g., with ovarian cancer) is contacted with a pair of oligonucleotide primers, under conditions that allow for the hybridization of the primers to nucleic acid template in the sample. The primers are extended under suitable conditions, dissociated from the template, and then re-annealed, extended, and dissociated to amplify the number of copies of the nucleic acid. The product of a PCR can be characterized by methods known in the art such as electrophoresis, restriction endonuclease cleavage patterns, oligonucleotide hybridization or ligation, and/or nucleic acid sequencing, using standard techniques.

Primers: Short nucleic acid molecules, for instance DNA oligonucleotides 10-100 nucleotides in length, such as about 15, 20, 25, 30 or 50 nucleotides or more in length. Primers can be annealed to a complementary target DNA strand (such as a gene listed in Table 1) by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand. Primer pairs can be used for amplification of a nucleic acid sequence, such as by PCR or other nucleic acid amplification methods known in the art.

Methods for preparing and using nucleic acid primers are described, for example, in Sambrook et al. (In Molecular Cloning: A Laboratory Manual, CSHL, New York, 1989), Ausubel et al. (ed.) (In Current Protocols in Molecular Biology, John Wiley & Sons, New York, 1998), and Innis et al. (PCR Protocols, A Guide to Methods and Applications, Academic Press, Inc., San Diego, Calif., 1990). PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, ©1991, Whitehead Institute for Biomedical Research, Cambridge, Mass.). One of ordinary skill in the art will appreciate that the specificity of a particular primer increases with its length. Thus, for example, a primer including 30 consecutive nucleotides of an ovarian endothelial cell tumor-associated molecule will anneal to a target sequence, such as another homolog of the designated endothelial cell tumor-associated protein, with a higher specificity than a corresponding primer of only 15 nucleotides. Thus, in order to obtain greater specificity, primers can be selected that include at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50 or more consecutive nucleotides of an ovarian endothelial cell tumor-associated nucleotide sequence.

Prognosis: A prediction of the course of a disease, such as ovarian cancer. The prediction can include determining the likelihood of a subject to develop aggressive, recurrent disease, to survive a particular amount of time (e.g., determine the likelihood that a subject will survive 1, 2, 3 or 5 years), to respond to a particular therapy (e.g., chemotherapy), or combinations thereof.

Purified: The term “purified” does not require absolute purity; rather, it is intended as a relative term. Thus, for example, a purified protein preparation is one in which the protein referred to is more pure than the protein in its natural environment within a cell. For example, a preparation of a protein is purified such that the protein represents at least 50% of the total protein content of the preparation. Similarly, a purified oligonucleotide preparation is one in which the oligonucleotide is more pure than in an environment including a complex mixture of oligonucleotides.

Recombinant: A recombinant nucleic acid molecule is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination can be accomplished for example, by chemical synthesis or by the artificial manipulation of isolated segments of nucleic acid molecules, such as by genetic engineering techniques.

Sample (or biological sample): A biological specimen containing genomic DNA, RNA (including mRNA), protein, or combinations thereof, obtained from a subject. Examples include, but are not limited to, peripheral blood, urine, saliva, tissue biopsy, surgical specimen, amniocentesis samples and autopsy material. In one example, a sample includes an ovarian cancer tissue biopsy.

Sensitivity: A measurement of activity, such as biological activity, of a molecule or a collection of molecules in a given condition. In an example, sensitivity refers to the activity of an agent, such as a binding agent that preferentially binds to one or more ovarian endothelial cell tumor-associated molecules, to alter the growth, development or progression of a disease, such as ovarian cancer. In certain examples, sensitivity or responsiveness can be assessed using any endpoint indicating a benefit to the subject, including, without limitation, (1) inhibition, to some extent, of tumor growth, including slowing down and complete growth arrest; (2) reduction in the number of tumor cells; (3) reduction in tumor size; (4) inhibition (such as reduction, slowing down or complete stopping) of tumor cell infiltration into adjacent peripheral organs and/or tissues; (5) inhibition (such as reduction, slowing down or complete stopping) of metastasis; (6) enhancement of anti-tumor immune response, which may, but does not have to, result in the regression or rejection of the tumor; (7) relief, to some extent, of one or more symptoms associated with the tumor; (8) increase in the length of survival following treatment; (9) decreased mortality at a given point of time following treatment; and/or (10) reducing or inhibiting angiogenesis.

Sequence identity/similarity: The identity/similarity between two or more nucleic acid sequences, or two or more amino acid sequences, is expressed in terms of the identity or similarity between the sequences. Sequence identity can be measured in terms of percentage identity; the higher the percentage, the more identical the sequences are. Sequence similarity can be measured in terms of percentage similarity (which takes into account conservative amino acid substitutions); the higher the percentage, the more similar the sequences are. Homologs or orthologs of nucleic acid or amino acid sequences possess a relatively high degree of sequence identity/similarity when aligned using standard methods. This homology is more significant when the orthologous proteins or cDNAs are derived from species which are more closely related (such as human and mouse sequences), compared to species more distantly related (such as human and C. elegans sequences).

Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith & Waterman, Adv. Appl. Math. 2:482, 1981; Needleman & Wunsch, J. Mol. Biol. 48:443, 1970; Pearson & Lipman, Proc. Natl. Acad. Sci. USA 85:2444, 1988; Higgins & Sharp, Gene, 73:237-44, 1988; Higgins & Sharp, CABIOS 5:151-3, 1989; Corpet et al., Nuc. Acids Res. 16:10881-90, 1988; Huang et al. Computer Appls. in the Biosciences 8, 155-65, 1992; and Pearson et al., Meth. Mol. Bio. 24:307-31, 1994. Altschul et al., J. Mol. Biol. 215:403-10, 1990, presents a detailed consideration of sequence alignment methods and homology calculations.

The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul et al., J. Mol. Biol. 215:403-10, 1990) is available from several sources, including the National Center for Biological Information (NCBI, National Library of Medicine, Building 38A, Room 8N805, Bethesda, Md. 20894) and on the Internet, for use in connection with the sequence analysis programs blastp, blastn, blastx, tblastn and tblastx. Additional information can be found at the NCBI web site.

BLASTN is used to compare nucleic acid sequences, while BLASTP is used to compare amino acid sequences. If the two compared sequences share homology, then the designated output file will present those regions of homology as aligned sequences. If the two compared sequences do not share homology, then the designated output file will not present aligned sequences.

Once aligned, the number of matches is determined by counting the number of positions where an identical nucleotide or amino acid residue is presented in both sequences. The percent sequence identity is determined by dividing the number of matches either by the length of the sequence set forth in the identified sequence, or by an articulated length (such as 100 consecutive nucleotides or amino acid residues from a sequence set forth in an identified sequence), followed by multiplying the resulting value by 100. For example, a nucleic acid sequence that has 1166 matches when aligned with a test sequence having 1154 nucleotides is 75.0 percent identical to the test sequence (1166÷1554*100=75.0). The percent sequence identity value is rounded to the nearest tenth. For example, 75.11, 75.12, 75.13, and 75.14 are rounded down to 75.1, while 75.15, 75.16, 75.17, 75.18, and 75.19 are rounded up to 75.2. The length value will always be an integer. In another example, a target sequence containing a 20-nucleotide region that aligns with 20 consecutive nucleotides from an identified sequence as follows contains a region that shares 75 percent sequence identity to that identified sequence (that is, 15÷20*100=75).

For comparisons of amino acid sequences of greater than about 30 amino acids, the Blast 2 sequences function is employed using the default BLOSUM62 matrix set to default parameters, (gap existence cost of 11, and a per residue gap cost of 1). Homologs are typically characterized by possession of at least 70% sequence identity counted over the full-length alignment with an amino acid sequence using the NCBI Basic Blast 2.0, gapped blastp with databases such as the nr or swissprot database. Queries searched with the blastn program are filtered with DUST (Hancock and Armstrong, 1994, Comput. Appl. Biosci. 10:67-70). Other programs use SEG. In addition, a manual alignment can be performed. Proteins with even greater similarity will show increasing percentage identities when assessed by this method, such as at least about 75%, 80%, 85%, 90%, 95%, 98%, or 99% sequence identity with the proteins listed in Table 1.

When aligning short peptides (fewer than around 30 amino acids), the alignment is be performed using the Blast 2 sequences function, employing the PAM30 matrix set to default parameters (open gap 9, extension gap 1 penalties). Proteins with even greater similarity to the reference sequence will show increasing percentage identities when assessed by this method, such as at least about 60%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% sequence identity with the proteins listed in Table 1. When less than the entire sequence is being compared for sequence identity, homologs will typically possess at least 75% sequence identity over short windows of 10-20 amino acids, and can possess sequence identities of at least 85%, 90%, 95% or 98% depending on their identity to the reference sequence. Methods for determining sequence identity over such short windows are described at the NCBI web site.

One indication that two nucleic acid molecules are closely related is that the two molecules hybridize to each other under stringent conditions, as described above. Nucleic acid sequences that do not show a high degree of identity may nevertheless encode identical or similar (conserved) amino acid sequences, due to the degeneracy of the genetic code. Changes in a nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid molecules that all encode substantially the same protein. Such homologous nucleic acid sequences can, for example, possess at least about 60%, 70%, 80%, 90%, 95%, 98%, or 99% sequence identity with the genes listed in Table 1 as determined by this method. An alternative (and not necessarily cumulative) indication that two nucleic acid sequences are substantially identical is that the polypeptide which the first nucleic acid encodes is immunologically cross reactive with the polypeptide encoded by the second nucleic acid.

One of skill in the art will appreciate that the particular sequence identity ranges are provided for guidance only; it is possible that strongly significant homologs could be obtained that fall outside the ranges provided.

Short interfering RNA (siRNA): A double stranded nucleic acid molecule capable of RNA interference or “RNAi.” (See, for example, Bass Nature 411: 428-429, 2001; Elbashir et al., Nature 411: 494-498, 2001; and Kreutzer et al., International PCT Publication No. WO 00/44895; Zernicka-Goetz et al., International PCT Publication No. WO 01/36646; Fire, International PCT Publication No. WO 99/32619; Plaetinck et al., International PCT Publication No. WO 00/01846; Mello and Fire, International PCT Publication No. WO 01/29058; Deschamps-Depaillette, International PCT Publication No. WO 99/07409; and Li et al., International PCT Publication No. WO 00/44914.) As used herein, siRNA molecules need not be limited to those molecules containing only RNA, but further encompasses chemically modified nucleotides and non-nucleotides having RNAi capacity or activity. In an example, an siRNA molecule is one that reduces or inhibits the biological activity or expression of one or more ovarian endothelial cell tumor-associated molecules disclosed in Tables 1, 2, 4 or 5 that are upregulated in ovarian tumor endothelial cells, such as EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, PLXDC1, EZH2, the Notch ligand Jagged1 or PTK2.

Specific Binding Agent: An agent that binds substantially or preferentially only to a defined target (for example, those listed in Table 1), such as a protein, enzyme, polysaccharide, oligonucleotide, DNA, RNA, recombinant vector or a small molecule. In an example, a “specific binding agent” is capable of binding to at least one of the disclosed ovarian endothelial cell tumor-associated molecules. Thus, a RNA-specific binding agent binds substantially only to the defined RNA, or to a specific region within the RNA. For example, a “specific binding agent” includes a siRNA that binds substantially to a specified RNA.

A protein-specific binding agent binds substantially only the defined protein, or to a specific region within the protein. For example, a “specific binding agent” includes antibodies and other agents that bind substantially to a specified polypeptide. The antibodies can be monoclonal or polyclonal antibodies that are specific for the polypeptide, as well as immunologically effective portions (“fragments”) thereof. The determination that a particular agent binds substantially only to a specific polypeptide may readily be made by using or adapting routine procedures. One suitable in vitro assay makes use of the Western blotting procedure (described in many standard texts, including Harlow and Lane, Using Antibodies: A Laboratory Manual, CSHL, New York, 1999).

Stanniocalcin 1 (STC1): A hormone that plays a role in calcium regulation, phosphate homeostasis and cell metabolism. In particular examples, expression of STC1 is increased in ovarian tumor endothelial cells. The term STC1 includes any STC1 gene, cDNA, mRNA, or protein from any organism and that is STC1 and is expressed or overexpressed in some examples in ovarian tumor endothelial cells.

Nucleic acid and protein sequences for STC1 are publicly available. For example, GenBank Accession Nos.: NM_(—)009285, NM_(—)00003155, and NM_(—)031123 disclose STC1 nucleic acid sequences, and GenBank Accession Nos.: AAH21425, NP_(—)112385, and NP_(—)033311 disclose STC1 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, STC1 includes a full-length wild-type (or native) sequence, as well as STC1 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, STC1 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: AAH21425, NP_(—)112385, or NP_(—)033311. In other examples, STC1 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 230746_s_at, 204595_s_at, and 204597_x_at and retains STC1 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Subject: Living multi-cellular vertebrate organisms, a category that includes human and non-human mammals.

Target sequence: A sequence of nucleotides located in a particular region in the human genome that corresponds to a desired sequence, such as an ovarian endothelial cell tumor-associated sequence. The target can be for instance a coding sequence; it can also be the non-coding strand that corresponds to a coding sequence. Examples of target sequences include those sequences associated with ovarian tumor endothelial cells, such as any of those listed in Tables 1 through 5.

Therapeutically Effective Amount: An amount of a composition that alone, or together with an additional therapeutic agent(s) (for example a chemotherapeutic agent), induces the desired response (e.g., treatment of a tumor). The preparations disclosed herein are administered in therapeutically effective amounts.

In one example, a desired response is to decrease ovarian tumor size or metastasis in a subject to whom the therapy is administered. Tumor metastasis does not need to be completely eliminated for the composition to be effective. For example, a composition can decrease metastasis by a desired amount, for example by at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination of the tumor), as compared to metastasis in the absence of the composition.

In particular examples, it is an amount of the therapeutic agent conjugated to the specific binding agent effective to decrease a number of ovarian cancer cells, such as in a subject to whom it is administered, for example a subject having one or more ovarian carcinomas. The cancer cells do not need to be completely eliminated for the composition to be effective. For example, a composition can decrease the number of cancer cells or growth of such cells by a desired amount, for example by at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination of detectable cancer cells), as compared to the number of cancer cells in the absence of the composition.

In other examples, it is an amount of the specific binding agent for one or more of the disclosed ovarian endothelial cell tumor-associated molecules capable of reducing angiogenesis by least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination of detectable angiogenesis) by the specific binding agent, or both, effective to decrease the metastasis of a tumor.

A therapeutically effective amount of a specific binding agent for at least one of the disclosed ovarian endothelial cell tumor-associated molecules, or cancer cells lysed by a therapeutic molecule conjugated to the agent, can be administered in a single dose, or in several doses, for example daily, during a course of treatment. However, the therapeutically effective amount can depend on the subject being treated, the severity and type of the condition being treated, and the manner of administration. For example, a therapeutically effective amount of such agent can vary from about 1 μg-10 mg per 70 kg body weight if administered intravenously and about 10 μg-100 mg per 70 kg body weight if administered intratumorally.

Tissue: A plurality of functionally related cells. A tissue can be a suspension, a semi-solid, or solid. Tissue includes cells collected from a subject such as the ovaries.

Treating a disease: “Treatment” refers to a therapeutic intervention that ameliorates a sign or symptom of a disease or pathological condition, such as a sign or symptom of ovarian cancer. Treatment can also induce remission or cure of a condition, such as ovarian cancer. In particular examples, treatment includes preventing a disease, for example by inhibiting the full development of a disease. Prevention of a disease does not require a total absence of disease. For example, a decrease of at least 50% can be sufficient.

Tumor: All neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. In an example, a tumor is an ovarian tumor.

Tumor-necrosis factor, alpha-induced protein 6 (TNFAIP6): A protein capable of regulating the expression of various molecules involved in the control of inflammation. In particular examples, expression of TNFAIP6 is increased in ovarian cancer endothelial cells. The term TNFAIP6 includes any TNFAIP6 gene, cDNA, mRNA, or protein from any organism and that is TNFAIP6 and is expressed or overexpressed in some examples in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for TNFAIP6 are publicly available. For example, GenBank Accession Nos.: NM_(—)007115, BC021155 and NM_(—)009398 disclose TNFAIP6 nucleic acid sequences, and GenBank Accession Nos.: AAH21155, NP_(—)009046 and NP_(—)033424 disclose TNFAIP6 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, TNFAIP6 includes a full-length wild-type (or native) sequence, as well as TNFAIP6 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as suppression of vascular growth. In certain examples, TNFAIP6 has at least 80% sequence identity, for example, at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: AAH21155, NP_(—)009046 or NP_(—)033424. In other examples, TNFAIP6 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 206026_s_at and retains TNFAIP6 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Twist homologue 1 (TWIST1): Overexpression of TWIST1 has been reported to play a role in destabilizing the genome, thus promoting chromosomal instability. For example, TWIST1 is capable of inhibiting chrondrogenesis. TWIST1 protein has also been noted to be involved in the regulation of tumor necrosis factor alpha production by antiinflammatory factors and pathways. In particular examples, expression of TWIST1 is increased in ovarian cancer endothelial cells. The term TWIST1 includes any TWIST1 gene, cDNA, mRNA, or protein from any organism and that is TWIST1 and is expressed or overexpressed in some examples in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for TWIST1 are publicly available. For example, GenBank Accession Nos.: NM_(—)000474, NM_(—)053530 and XM_(—)001076553 and disclose TWIST1 nucleic acid sequences, and GenBank Accession Nos.: NP_(—)000465 and ABM87769 disclose TWIST1 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, TWIST1 includes a full-length wild-type (or native) sequence, as well as TWIST1 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, TWIST1 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: NP_(—)000465 or ABM87769. In other examples, TWIST1 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 206026_s_at and retains TWIST1 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Under conditions sufficient for: A phrase that is used to describe any environment that permits the desired activity. In one example, includes administering a test agent to an ovarian cancer cell or a subject sufficient to allow the desired activity. In particular examples, the desired activity is altering the activity (such as the expression) of an ovarian endothelial cell tumor-associated molecule.

Unit dose: A physically discrete unit containing a predetermined quantity of an active material calculated to individually or collectively produce a desired effect, such as a therapeutic effect. A single unit dose or a plurality of unit doses can be used to provide the desired effect, such as treatment of a tumor, for example a metastatic tumor. In one example, a unit dose includes a desired amount of an agent that decreases or inhibits angiogenesis.

Upregulated or activation: When used in reference to the expression of a nucleic acid molecule, such as a gene, refers to any process which results in an increase in production of a gene product. A gene product can be RNA (such as mRNA, rRNA, tRNA, and structural RNA) or protein. Therefore, gene upregulation or activation includes processes that increase transcription of a gene or translation of mRNA. Specific examples of ovarian endothelial cell tumor-associated molecules that are up-regulated in ovarian tumor endothelial cells are provided in Tables 2 and 4. For example, EZH2, EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, and PLXDC1 are upregulated or increased in expression in ovarian tumor endothelial cells.

Examples of processes that increase transcription include those that facilitate formation of a transcription initiation complex, those that increase transcription initiation rate, those that increase transcription elongation rate, those that increase processivity of transcription and those that relieve transcriptional repression (for example by blocking the binding of a transcriptional repressor). Gene upregulation can include inhibition of repression as well as stimulation of expression above an existing level. Examples of processes that increase translation include those that increase translational initiation, those that increase translational elongation and those that increase mRNA stability.

Gene upregulation includes any detectable increase in the production of a gene product. In certain examples, production of a gene product increases by at least 2-fold, for example at least 3-fold or at least 4-fold, as compared to a control (such an amount of gene expression in a normal endothelial cell). In one example, a control is a relative amount of gene expression in a biological sample, such as in an ovarian tissue biopsy obtained from a subject that does not have ovarian cancer.

Vasohibin 1 (VASH1): a protein that is expressed in a variety of tissues and inhibits functions relevant to neovascularization (migration, proliferation, and network formation by endothelial cells). Vasohibin also inhibits angiogenesis in vivo. The unglycosylated protein (42 kDa) does not contain a classical secretory secretion sequence and appears in the medium as a protein of 30 kDa, suggesting proteolytic processing during secretion. In particular examples, VASH1 is regulated by EZH2 wherein EZH2 binds to the VASH1 promoter and decreases or inhibits VASH1 anti-angiogenesis activity. The term VASH1 includes any VASH1 gene, cDNA, mRNA, or protein from any organism and that is VASH1 and is expressed or overexpressed in some examples in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for VASH1 are publicly available. For example, GenBank Accession Nos.: NP_(—)055724 (human); NP_(—)796328 (mouse); and NP_(—)659128 disclose VASH1 amino acid sequences which are incorporated by reference as provided by GenBank on Aug. 14, 2009. Further, GenBank Accession Nos.: NM_(—)014909 (human) and NM_(—)177354 (mouse) disclose nucleic acid sequences which are incorporated by reference as provided by GenBank on Aug. 14, 2009.

In one example, vasohibin includes a full-length wild-type (or native) sequence, as well as VASH1 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, VASH1 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: NP_(—)055724; NP_(—)796328 or NP_(—)659128 and retains VASH1 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Zeste homologue 2 (EZH2): A member of the polycomb group of genes that has been reported to be involved in cell cycle regulation. EZH2, a component of the polycomb repressive complex 2 (PRC2), has intrinsic histone methyl transferase (HMTase) activity and has been implicated in the progression and metastasis of several cancers. EZH2 is also a transcriptional repressor that has multiple targets, including anti-angiogenic, pro-apoptotic, and tumor suppressor genes. In particular examples, expression of EZH2 is increased in ovarian cancer endothelial cells. In one example, expression of EZH2 is an indicator of poor prognosis. The term EZH2 includes any EZH2 gene, cDNA, mRNA, or protein from any organism and that is EZH2 and is expressed or overexpressed in some examples in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for EZH2 are publicly available. For example, GenBank Accession Nos.: NM_(—)004456 and AY519465.1 disclose EZH2 nucleic acid sequences, and GenBank Accession No. AAS09975 discloses a EZH2 protein sequence, which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, EZH2 includes a full-length wild-type (or native) sequence, as well as EZH2 allelic variants, fragments, homologs or fusion sequences that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, EZH2 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to AAS09975. In other examples, EZH2 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 203358_s_at and retains EZH2 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Additional terms commonly used in molecular genetics can be found in Benjamin Lewin, Genes V published by Oxford University Press, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8).

Methods of Treatment

It is shown herein that ovarian cancer is associated with differential expression of ovarian endothelial cell tumor-associated molecules. For example, the disclosed gene expression profile has identified ovarian endothelial cell tumor-associated molecules. Based on these observations, methods of treatment to reduce or eliminate ovarian cancer are disclosed. For example, the method can include inhibiting the expression or biological activity of at least one of the ovarian endothelial cell tumor associated molecules from Tables 1, 2, 4, and/or 5 that are upregulated in ovarian tumor cells or increasing the expression or biological activity of at least one of the ovarian endothelial cell tumor associated molecules from Tables 1, 3 and/or 5 that are downregulated in ovarian tumor cells or combinations thereof. As used herein, “inhibit” does not require 100% inhibition of expression or activity. For example, a substantial reduction may be adequate, such as reduction in expression or activity of at least 20%, at least 30%, at least 50%, at least 75%, or at least 95% may be sufficient to obtain desired therapeutic results. In some examples, an “increase” in expression or activity is an increase of at least 20%, at least 30%, at least 50%, at least 75%, or at least 95%. In some embodiments, the subject is a human, but the subject can alternatively be a veterinary or laboratory subject. In some embodiments, the ovarian cancer is papillary serous ovarian cancer.

Methods are disclosed herein for treating an ovarian tumor, such as ovarian cancer. In one example, the method includes administering a therapeutically effective amount of a composition to a subject. The composition can include a binding agent that is specific for one of the ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4 or 5 that are upregulated in ovarian tumor cells. Administration of such compounds decreases the expression or activity of the molecule that is undesirably upregulated in ovarian cancer cells. The molecules in Tables 1, 2, 4, or 5 include, for instance, nucleic acid sequences (such as DNA, cDNA, or mRNAs) and proteins. Specific genes include those listed in Tables 1, 2, 4 or 5 as well as fragments of the full-length genes, cDNAs, or mRNAs (and proteins encoded thereby) whose expression is upregulated in response to an ovarian tumor, such as ovarian cancer.

In particular examples, the specific binding agent is an inhibitor such as a siRNA or an antibody to one of the disclosed ovarian endothelial cell tumor-associated molecules that is upregulated in ovarian tumor cells. For example, the specific binding agent can be a siRNA that interferes with mRNA expression of one of the disclosed ovarian endothelial cell tumor-associated molecules that are involved in angiogenesis, such as a molecule involved in regulating cell motility, cell proliferation or tube formation, thereby inhibiting cell motility, cell proliferation or tube formation. For example, the specific binding agent can be a siRNA that inhibits the expression of PTK2, EZH2 or Jagged1. In other particular examples, ovarian tumor growth is reduced or inhibited by administering a specific binding agent to inhibit or reduce the expression or production of EZH2, EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, and PLXDC1. In additional examples, a composition includes at least two specific binding agents such as two specific siRNAs that each bind to their respective ovarian endothelial cell tumor-associated nucleotide sequences and inhibit ovarian tumor growth in a subject. In some examples, the composition includes at least 2, 3, 4, 5, 5, 8 or 10 different siRNA molecules. For example, the composition can include PTK2, EZH2 and Jagged1 siRNAs.

Treating Ovarian Cancer by Altering Activity of an Ovarian Endothelial Cell Tumor-Associated Molecule

Methods are provided to inhibit ovarian endothelial cell tumor-associated molecule activity or expression to treat an ovarian tumor. Treatment of tumors by reducing the number of ovarian endothelial cell tumor-associated molecules can include delaying the development of the tumor in a subject (such as preventing metastasis of a tumor). Treatment of a tumor also includes reducing signs or symptoms associated with the presence of such a tumor (for example by reducing the size, growth or volume of the tumor or a metastasis thereof). Such reduced growth can in some examples decrease or slow metastasis of the tumor, or reduce the size or volume of the tumor by at least 10%, at least 20%, at least 50%, or at least 75%, such as by inhibiting angiogenesis by at least 10%, at least 20%, at least 50%, or at least 75%. For example, ovarian endothelial cell tumor-associated molecules involved in angiogenesis, such as molecules involved in promoting cell proliferation, cell motility or tube formation can be inhibited to treat an ovarian tumor, such as those provided in any of Tables 1, 2, 4 or 5 that are upregulated in ovarian endothelial tumor cells. In other examples, ovarian tumor growth is reduced or inhibited by inhibiting the expression or biological activity ovarian endothelial cell tumor-associated molecules provided in any of Tables 1, 2, 4 or 5 that are upregulated in ovarian tumor endothelial cells. In further examples, inhibition of ovarian endothelial cell tumor-associated molecules includes reducing the invasive activity of the tumor in the subject. In some examples, treatment using the methods disclosed herein prolongs the time of survival of the subject.

Specific Binding Agents

Specific binding agents are agents that selectively bind with higher affinity to a molecule of interest, than to other molecules. For example, a specific binding agent can be one that binds with high affinity to one of the genes or gene products of the ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4 or 5 that are upregulated in ovarian tumor endothelial cells, but does not substantially bind to another gene or gene product. In a specific example, a specific binding agent binds to one gene listed in Tables 1, 2, 4 or 5 that is upregulated in ovarian tumor endothelial cells thereby reducing or inhibiting expression of the gene, but does not bind to the other genes (or gene product) listed in such Tables under similar conditions. For example, the agent can interfere with gene expression (transcription, processing, translation, post-translational modification), such as, by interfering with the gene's mRNA and blocking translation of the gene product or by post-translational modification of a gene product, or by causing changes in intracellular localization. In another specific example, a specific binding agent binds to a protein encoded by of one of the genes listed in Table 1, 2, 4 or 5 that is upregulated in ovarian tumor endothelial cells with a binding affinity in the range of 0.1 to 20 nM and reduces or inhibits the activity of such protein.

Examples of specific binding agents include, but are not limited to, siRNAs, antibodies, ligands, recombinant proteins, peptide mimetics, and soluble receptor fragments. One example of a specific binding agent is a siRNA. Methods of making siRNA that can be used clinically are known in the art. Particular siRNAs and methods that can be used to produce and administer them are described in detail below. In some examples, the siRNA is incorporated into a chitosan (CH) nanoparticle, such as chitosan obtained from shellfish or fungi.

Another specific example of a specific binding agent is an antibody, such as a monoclonal or polyclonal antibody. Methods of making antibodies that can be used clinically are known in the art. Particular antibodies and methods that can be used to produce them are described in detail below.

In a further example, small molecular weight inhibitors or antagonists of the receptor protein can be used to regulate activity such as the expression or production of ovarian endothelial cell tumor-associated molecules. In a particular example, small molecular weight inhibitors or antagonists of the proteins encoded by the genes listed in Tables 2 and/or 4 are employed.

Specific binding agents can be therapeutic, for example by reducing or inhibiting the biological activity of a nucleic acid or protein. Complete inhibition is not required. For example, a reduction by at least 10%, at least 20%, at least 30%, at least 50%, at least 70%, or even at least 90% can be sufficient. For example, a specific binding agent that binds with high affinity to a gene listed in Tables 1, 2, 4 and/or 5 that are upregulated in ovarian tumor endothelial cells, may substantially reduce the biological function of the gene or gene product (for example, the ability of the gene or gene product to facilitate angiogenesis). In other examples, a specific binding agent that binds with high affinity to one of the proteins encoded by the genes listed in Tables 1, 2, 4 and/or 5 that are upregulated in ovarian tumor endothelial cells, may substantially reduce the biological function of the protein (for example, the ability of the protein to promote angiogenesis). Such agents can be administered in therapeutically effective amounts to subjects in need thereof, such as a subject having ovarian cancer, such as papillary serous ovarian cancer.

Pre-Screening Subjects

In some examples, subjects are initially screened to determine if they have ovarian cancer. In an example, subjects are initially screened for ovarian cancer by using one of the disclosed gene expression profiles (as discussed in detail below). In some examples, if one or more of the disclosed endothelial cell tumor-associated molecules upregulated in ovarian endothelial cells (such as those listed in Tables 2 and 4) is detected, a specific binding agent capable of reducing or inhibiting ovarian cancer is adminstered.

Pre-Screening Specific Binding Agents

In some examples, specific binding agents are initially screened for treating ovarian cancer by use of the disclosed gene expression profile (see below). For example, the disclosed gene expression profile can be used to identify specific binding agents capable of reducing or inhibiting ovarian cancer. In an example, the disclosed gene expression profile is used to identify compositions that can be employed to reduce or inhibit angiogenesis in ovarian tumors.

Exemplary Tumors

A tumor is an abnormal growth of tissue that results from excessive cell division. A particular example of a tumor is cancer. For example, the current application provides methods for the treatment (such as the prevention or reduction of metastasis) of tumors (such as cancers) by altering the expression/production of one or more disclosed ovarian endothelial cell tumor-associated molecules. In some examples, the tumor is treated in vivo, for example in a mammalian subject, such as a human subject. Exemplary tumors that can be treated using the disclosed methods include, but are not limited to ovarian cancer, including metastases of such tumors to other organs. Generally, the tumor is an ovarian cancer, such as papillary serous ovarian cancer.

Administration

Methods of administrating the disclosed compositions are routine, and can be determined by a skilled clinician. For example, the disclosed therapies (such as those that include a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules listed in Tables 1, 2, 4 or 5 whose expression is increased in ovarian endothelial tumor-associated cells) can be administered via injection, intratumorally, orally, topically, transdermally, parenterally, or via inhalation or spray. In a particular example, a composition is administered intravenously to a mammalian subject, such as a human.

The therapeutically effective amount of the agents administered can vary depending upon the desired effects and the subject to be treated. In one example, the method includes daily administration of at least 1 μg of the composition to the subject (such as a human subject). For example, a human can be administered at least 1 μg or at least 1 mg of the composition daily, such as 10 μg to 100 μg daily, 100 μg to 1000 μg daily, for example 10 μg daily, 100 μg daily, or 1000 μg daily. In one example, the subject is administered at least 1 μg (such as 1-100 μg) intravenously of the composition including a binding agent that specifically binds to one of the disclosed ovarian endothelial cell tumor-associated molecules provided herein. In one example, the subject is administered at least 1 mg intramuscularly (for example in an extremity) of such composition. In a specific example, the dose is 50 to 350 μg/kg twice weekly, such as 150 μg/kg twice weekly (for example via iv injection). The dosage can be administered in divided doses (such as 2, 3, or 4 divided doses per day), or in a single dosage daily.

In particular examples, the subject is administered the therapeutic composition that includes a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules on a multiple daily dosing schedule, such as at least two consecutive days, 10 consecutive days, and so forth, for example for a period of weeks, months, or years. In one example, the subject is administered the therapeutic composition that a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules daily for a period of at least 30 days, such as at least 2 months, at least 4 months, at least 6 months, at least 12 months, at least 24 months, or at least 36 months.

The therapeutic compositions, such as those that include a binding agent specific for one of the ovarian endothelial cell tumor-associated molecules, can further include one or more biologically active or inactive compounds (or both), such as anti-neoplastic agents and conventional non-toxic pharmaceutically acceptable carriers, respectively.

In a particular example, a therapeutic composition that includes a therapeutically effective amount of a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules further includes one or more biologically inactive compounds. Examples of such biologically inactive compounds include, but are not limited to: carriers, thickeners, diluents, buffers, preservatives, and carriers. The pharmaceutically acceptable carriers useful for these formulations are conventional (see Remington's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, Pa., 19th Edition (1995)). For solid compositions (for example, powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate. In addition to biologically-neutral carriers, pharmaceutical compositions to be administered can include minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.

Additional Treatments

In particular examples, prior to, during, or following administration of a therapeutic amount of an agent that reduces or inhibits ovarian cancer due to the interaction of a binding agent with one of the disclosed ovarian endothelial cell tumor-associated molecules, the subject can receive one or more other therapies. In one example, the subject receives one or more treatments to remove or reduce the tumor prior to administration of a therapeutic amount of a composition including a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules.

Examples of such therapies include, but are not limited to, surgical treatment for removal or reduction of the tumor (such as surgical resection, cryotherapy, or chemoembolization), as well as anti-tumor pharmaceutical treatments which can include radiotherapeutic agents, anti-neoplastic chemotherapeutic agents, antibiotics, alkylating agents and antioxidants, kinase inhibitors, and other agents. Particular examples of additional therapeutic agents that can be used include microtubule binding agents, DNA intercalators or cross-linkers, DNA synthesis inhibitors, DNA and/or RNA transcription inhibitors, antibodies, enzymes, enzyme inhibitors, and gene regulators. These agents (which are administered at a therapeutically effective amount) and treatments can be used alone or in combination. Methods and therapeutic dosages of such agents are known to those skilled in the art, and can be determined by a skilled clinician.

“Microtubule binding agent” refers to an agent that interacts with tubulin to stabilize or destabilize microtubule formation thereby inhibiting cell division. Examples of microtubule binding agents that can be used in conjunction with the disclosed therapy include, without limitation, paclitaxel, docetaxel, vinblastine, vindesine, vinorelbine (navelbine), the epothilones, colchicine, dolastatin 15, nocodazole, podophyllotoxin and rhizoxin. Analogs and derivatives of such compounds also can be used and are known to those of ordinary skill in the art. For example, suitable epothilones and epothilone analogs are described in International Publication No. WO 2004/018478. Taxoids, such as paclitaxel and docetaxel, as well as the analogs of paclitaxel taught by U.S. Pat. Nos. 6,610,860; 5,530,020; and 5,912,264 can be used.

The following classes of compounds are of use in the methods disclosed herein: Suitable DNA and/or RNA transcription regulators, including, without limitation, actinomycin D, daunorubicin, doxorubicin and derivatives and analogs thereof also are suitable for use in combination with the disclosed therapies. DNA intercalators and cross-linking agents that can be administered to a subject include, without limitation, cisplatin, carboplatin, oxaliplatin, mitomycins, such as mitomycin C, bleomycin, chlorambucil, cyclophosphamide and derivatives and analogs thereof. DNA synthesis inhibitors suitable for use as therapeutic agents include, without limitation, methotrexate, 5-fluoro-5′-deoxyuridine, 5-fluorouracil and analogs thereof. Examples of suitable enzyme inhibitors include, without limitation, camptothecin, etoposide, formestane, trichostatin and derivatives and analogs thereof. Suitable compounds that affect gene regulation include agents that result in increased or decreased expression of one or more genes, such as raloxifene, 5-azacytidine, 5-aza-2′-deoxycytidine, tamoxifen, 4-hydroxytamoxifen, mifepristone and derivatives and analogs thereof. Kinase inhibitors include Gleevac, Iressa, and Tarceva that prevent phosphorylation and activation of growth factors.

Other therapeutic agents, for example anti-tumor agents, that may or may not fall under one or more of the classifications above, also are suitable for administration in combination with the disclosed therapies. By way of example, such agents include adriamycin, apigenin, rapamycin, zebularine, cimetidine, and derivatives and analogs thereof.

In one example, the therapeutic composition (such as one including a binding agent specific for one or more of the disclosed ovarian endothelial cell tumor-associated molecules) is injected into the subject in the presence of an adjuvant. An adjuvant is an agent that when used in combination with an immunogenic agent augments or otherwise alters or modifies a resultant immune response. In some examples, an adjuvant increases the titer of antibodies induced in a subject by the immunogenic agent. In one example, the one or more peptides are administered to the subject as an emulsion with an adjuvant and sterile water for injection (for example an intravenous or intramuscular injection). Incomplete Freund's Adjuvant (Seppic, Inc.) can be used as the Freund's Incomplete Adjuvant (IFA) (Fairfield, N.J.). In some examples, IFA is provided in 3 ml of a mineral oil solution based on mannide oleate (Montanide ISA-51). At the time of injection, the peptide(s) is mixed with the Montanide ISA.51 and then administered to the subject. Other adjuvants can be used, for example, Freund's complete adjuvant, B30-MDP, LA-15-PH, montanide, saponin, aluminum hydroxide, alum, lipids, keyhole lympet protein, hemocyanin, a mycobacterial antigen, and combinations thereof.

In some examples, the subject receiving the therapeutic peptide composition (such as one including a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules) is also administered interleukin-2 (IL-2), for example via intravenous administration. In particular examples, IL-2 (Chiron Corp., Emeryville, Calif.) is administered at a dose of at least 500,000 IU/kg as an intravenous bolus over a 15 minute period every eight hours beginning on the day after administration of the peptides and continuing for up to 5 days. Doses can be skipped depending on subject tolerance.

In some examples, the disclosed compositions can be co-administered with a fully human antibody to cytotoxic T-lymphocyte antigen-4 (anti-CTLA-4). In some example subjects receive at least 1 mg/kg anti-CTLA-4 (such as 3 mg/kg every 3 weeks or 3 mg/kg as the initial dose with subsequent doses reduced to 1 mg/kg every 3 weeks).

In one example, at least a portion of the ovarian tumor (such as a metastatic tumor) is surgically removed (for example via cryotherapy), irradiated, chemically treated (for example via chemoembolization) or combinations thereof, prior to administration of the disclosed therapies (such as administration of a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules). For example, a subject having a metastatic tumor can have all or part of the tumor surgically excised prior to administration of the disclosed therapies (such as one including a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules). In an example, one or more chemotherapeutic agents is administered following treatment with a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules. In another particular example, the subject has a metastatic tumor and is administered radiation therapy, chemoembolization therapy, or both concurrently with the administration of the disclosed therapies (such as one including a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules).

Generation and Administration of siRNA

In an example, certain inhibitors provided by this disclosure are species of siRNAs. One of ordinary skill in the art can readily generate siRNAs which specifically bind to one of the disclosed ovarian endothelial cell tumor-associated molecules that are upregulated in ovarian endothelial cell tumor cells. In an example, commercially available kits, such as siRNA molecule synthesizing kits from PROMEGA® (Madison, Wis.) or AMBION® (Austin, Tex.) may be used to synthesize siRNA molecules. In another example, siRNAs are obtained from commercial sources, such as from QIAGEN® Inc (Germantown, Md.), INVITROGEN® (Carlsbad, Calif.), AMBION (Austin, Tex.), DHARMACON® (Lafayette, Colo.) or OPENBIOSYSTEMS® (Huntsville, Ala.).

In certain examples, expression vectors are employed to express the at least one siRNA molecule. For example, an expression vector can include a nucleic acid sequence encoding at least one siRNA molecule corresponding to at least one of the disclosed ovarian endothelial cell tumor-associated molecules listed in Tables 1, 2, 4 and/or Table 5 that are upregulated in ovarian endothelial cell tumor cells. For example, siRNA specific for EZH2 can be generated using publicly available EZH2 nucleic acid sequences, such as those described above. In a particular example, the vector contains a sequence(s) encoding both strands of a siRNA molecule comprising a duplex. In another example, the vector also contains sequence(s) encoding a single nucleic acid molecule that is self-complementary and thus forms a siRNA molecule. Non-limiting examples of such expression vectors are described in Paul et al., Nature Biotechnology 19:505, 2002; Miyagishi and Taira, Nature Biotechnology 19:497, 2002; Lee et al., Nature Biotechnology 19:500, 2002; and Novina et al., Nature Medicine, online publication Jun. 3, 2003.

In other examples, siRNA molecules include a delivery vehicle, including inter alia liposomes, for administration to a subject, carriers and diluents and their salts, and can be present in pharmaceutical compositions. Nucleic acid molecules can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other delivery vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors (see, for example, O'Hare and Normand, International PCT Publication No. WO 00/53722). In one specific example, siRNAs are administered at according to the teachings of Soutschek et al. (Nature Vol. 432: 173-178, 2004) or Karpilow et al. (Pharma Genomics 32-40, 2004) both of which are herein incorporated by reference in their entireties.

In some examples, siRNAs are incorporated into neutral liposomes, such as DOPC or chitosan, and injected intraperitoneal or intravenously. For example, a siRNA can be administered at at least 1 μg/kg twice weekly, such as at least 50 μg/kg twice weekly, at least 100 μg/kg twice weekly, at least 125 μg/kg twice weekly, at least 150 μg/kg twice weekly, at least 200 μg/kg twice weekly for at least 1 week, such as at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 6 weeks, at least 12 weeks, or at least 24 weeks. In one example, about at least 1-500 μg/kg, such 10-250 μg/kg, is adminstered at least twice weekly for at least 1 week, such as at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 6 weeks, at least 12 weeks, or at least 24 weeks. In a certain example, approximately 150 μg/kg is administered twice weekly, for 2 to 3 weeks. In other examples, approximately 1 ug/kg daily for 3 weeks or 50 ug/kg every other day for 3 weeks is administered.

Alternatively, the nucleic acid/vehicle combination can be locally delivered by direct injection or by use of an infusion pump. Direct injection of the nucleic acid molecules of the disclosure, whether subcutaneous, intramuscular, or intradermal, can take place using standard needle and syringe methodologies, or by needle-free technologies such as those described by Barry et al., International PCT Publication No. WO 99/31262. Other delivery routes, but are not limited to, oral delivery (such as in tablet or pill form), intrathecal or intraperitoneal delivery. For example, intraperitoneal delivery can take place by injecting the treatment into the peritoneal cavity of the subject in order to directly deliver the molecules to the tumor site. More detailed descriptions of nucleic acid delivery and administration are provided in Sullivan et al., PCT WO 94/02595, Draper et al., PCT WO93/23569, Beigelman et al., PCT WO99/05094, and Klimuk et al., PCT WO99/04819, all of which are incorporated by reference herein.

Alternatively, certain siRNA molecules can be expressed within cells from eukaryotic promoters. Those skilled in the art will recognize that any nucleic acid can be expressed in eukaryotic cells using the appropriate DNA/RNA vector. The activity of such nucleic acids can be augmented by their release from the primary transcript by an enzymatic nucleic acid (Draper et al., PCT WO 93/23569, and Sullivan et al., PCT WO 94/02595).

In other examples, siRNA molecules can be expressed from transcription units (see for example, Couture et al., 1996, TIG 12:510) inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. siRNA expressing viral vectors can be constructed based on, for example, but not limited to, adeno-associated virus, retrovirus, adenovirus, lentivirus or alphavirus. In another example, pol III based constructs are used to express nucleic acid molecules (see for example, Thompson, U.S. Pat. Nos. 5,902,880 and 6,146,886).

The recombinant vectors capable of expressing the siRNA molecules can be delivered as described above, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of nucleic acid molecules. Such vectors can be repeatedly administered as necessary. Once expressed, the siRNA molecule interacts with the target mRNA and generates an RNAi response. Delivery of siRNA molecule expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell.

Generation of Antibodies

One of ordinary skill in the art can readily generate antibodies which specifically bind to the disclosed ovarian endothelial cell tumor-associated molecules. These antibodies can be monoclonal or polyclonal. They can be chimeric or humanized. Any functional fragment or derivative of an antibody can be used including Fab, Fab′, Fab2, Fab′2, and single chain variable regions. So long as the fragment or derivative retains specificity of binding for the ovarian endothelial cell tumor-associated molecule it can be used in the methods provided herein. Antibodies can be tested for specificity of binding by comparing binding to appropriate antigen to binding to irrelevant antigen or antigen mixture under a given set of conditions. If the antibody binds to appropriate antigen at least 2, at least 5, at least 7 or 10 times more than to irrelevant antigen or antigen mixture, then it is considered to be specific.

In an example, monoclonal antibodies are generated to the ovarian endothelial cell tumor-associated molecules disclosed in Tables 1, 2, 4 or 5 that are upregulated in ovarian endothelial cell tumor cells. These monoclonal antibodies each include a variable heavy (V_(H)) and a variable light (V_(L)) chain and specifically bind to the specific ovarian endothelial cell tumor-associated molecules. For example, the antibody can bind the specific ovarian endothelial cell tumor-associated molecules with an affinity constant of at least 10⁶ M⁻¹, such as at least 10⁷ M⁻¹, at least 10⁸ M⁻¹, at least 5×10⁸ M⁻¹, or at least 10⁹ M⁻¹.

The specific antibodies can include a V_(L) polypeptide having amino acid sequences of the complementarity determining regions (CDRs) that are at least about 90% identical, such as at least about 95%, at least about 98%, or at least about 99% identical to the amino acid sequences of the specific ovarian endothelial cell tumor-associated molecules and a V_(H) polypeptide having amino acid sequences of the CDRs that are at least about 90% identical, such as at least about 95%, at least about 98%, or at least about 99% identical to the amino acid sequences of the specific ovarian endothelial cell tumor-associated molecules.

In one example, the sequence of the specificity determining regions of each CDR is determined. Residues that are outside the SDR (non-ligand contacting sites) are substituted. For example, in any of the CDR sequences, at most one, two or three amino acids can be substituted. The production of chimeric antibodies, which include a framework region from one antibody and the CDRs from a different antibody, is well known in the art. For example, humanized antibodies can be routinely produced. The antibody or antibody fragment can be a humanized immunoglobulin having CDRs from a donor monoclonal antibody that binds one of the disclosed ovarian endothelial cell tumor-associated molecules and immunoglobulin and heavy and light chain variable region frameworks from human acceptor immunoglobulin heavy and light chain frameworks. Generally, the humanized immunoglobulin specifically binds to one of the disclosed ovarian endothelial cell tumor-associated molecules with an affinity constant of at least 10⁷ M⁻¹, such as at least 10⁸ M⁻¹ at least 5×10⁸ M⁻¹ or at least 10⁹ M⁻¹.

In another example, human monoclonal antibodies to the disclosed ovarian endothelial cell tumor-associated molecules in Tables 1, 2, 4 and 5 that are upregulated in ovarian endothelial tumor cells are produced. Human monoclonal antibodies can be produced by transferring donor complementarity determining regions (CDRs) from heavy and light variable chains of the donor mouse immunoglobulin into a human variable domain, and then substituting human residues in the framework regions when required to retain affinity. The use of antibody components derived from humanized monoclonal antibodies obviates potential problems associated with the immunogenicity of the constant regions of the donor antibody. For example, when mouse monoclonal antibodies are used therapeutically, the development of human anti-mouse antibodies (HAMA) leads to clearance of the murine monoclonal antibodies and other possible adverse events. Chimeric monoclonal antibodies, with human constant regions, humanized monoclonal antibodies, retaining only murine CDRs, and “fully human” monoclonal antibodies made from phage libraries or transgenic mice have all been used to reduce or eliminate the murine content of therapeutic monoclonal antibodies.

Techniques for producing humanized monoclonal antibodies are described, for example, by Jones et al., Nature 321:522, 1986; Riechmann et al., Nature 332:323, 1988; Verhoeyen et al., Science 239:1534, 1988; Carter et al., Proc. Natl. Acad. Sci. U.S.A. 89:4285, 1992; Sandhu, Crit. Rev. Biotech. 12:437, 1992; and Singer et al., J. Immunol. 150:2844, 1993. The antibody may be of any isotype, but in several embodiments the antibody is an IgG, including but not limited to, IgG₁, IgG₂, IgG₃ and IgG₄.

In one example, the sequence of the humanized immunoglobulin heavy chain variable region framework can be at least about 65% identical to the sequence of the donor immunoglobulin heavy chain variable region framework. Thus, the sequence of the humanized immunoglobulin heavy chain variable region framework can be at least about 75%, at least about 85%, at least about 99% or at least about 95%, identical to the sequence of the donor immunoglobulin heavy chain variable region framework. Human framework regions, and mutations that can be made in a humanized antibody framework regions, are known in the art (see, for example, in U.S. Pat. No. 5,585,089).

Antibodies, such as murine monoclonal antibodies, chimeric antibodies, and humanized antibodies, include full length molecules as well as fragments thereof, such as Fab, F(ab′)₂, and Fv, which include a heavy chain and light chain variable region and are capable of binding the epitopic determinant. These antibody fragments retain some ability to selectively bind with their epitope. These fragments include: (1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule, can be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain; (2) Fab′, the fragment of an antibody molecule can be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab′ fragments are obtained per antibody molecule; (3) (Fab′)₂, the fragment of the antibody that can be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; F(ab′)₂ is a dimer of two Fab′ fragments held together by two disulfide bonds; (4) Fv, a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and (5) Single chain antibody (such as scFv), defined as a genetically engineered molecule containing the variable region of the light chain, the variable region of the heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule. Methods of making these fragments are known in the art (see for example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York, 1988. Fv antibodies are typically about 25 kDa and contain a complete antigen-binding site with three CDRs per each heavy chain and each light chain. To produce these antibodies, the V_(H) and the V_(L) can be expressed from two individual nucleic acid constructs in a host cell. If the V_(H) and the V_(L) are expressed non-contiguously, the chains of the Fv antibody are typically held together by noncovalent interactions. However, these chains tend to dissociate upon dilution, so methods have been developed to crosslink the chains through glutaraldehyde, intermolecular disulfides, or a peptide linker Thus, in one example, the Fv can be a disulfide stabilized Fv (dsFv), wherein the heavy chain variable region and the light chain variable region are chemically linked by disulfide bonds.

In an additional example, the Fv fragments include V_(H) and V_(L) chains connected by a peptide linker These single-chain antigen binding proteins (scFv) are prepared by constructing a structural gene comprising DNA sequences encoding the V_(H) and V_(L) domains connected by an oligonucleotide. The structural gene is inserted into an expression vector, which is subsequently introduced into a host cell such as E. coli. The recombinant host cells synthesize a single polypeptide chain with a linker peptide bridging the two V domains. Methods for producing scFvs are known in the art (see Whitlow et al., Methods: a Companion to Methods in Enzymology, Vol. 2, page 97, 1991; Bird et al., Science 242:423, 1988; U.S. Pat. No. 4,946,778; Pack et al., Bio/Technology 11:1271, 1993; and Sandhu, supra).

Antibody fragments can be prepared by proteolytic hydrolysis of the antibody or by expression in E. coli of DNA encoding the fragment. Antibody fragments can be obtained by pepsin or papain digestion of whole antibodies by conventional methods. For example, antibody fragments can be produced by enzymatic cleavage of antibodies with pepsin to provide a 5S fragment denoted F(ab′)₂. This fragment can be further cleaved using a thiol reducing agent, and optionally a blocking group for the sulfhydryl groups resulting from cleavage of disulfide linkages, to produce 3.5S Fab′ monovalent fragments. Alternatively, an enzymatic cleavage using pepsin produces two monovalent Fab′ fragments and an Fc fragment directly (see U.S. Pat. No. 4,036,945 and U.S. Pat. No. 4,331,647, and references contained therein; Nisonhoff et al., Arch. Biochem. Biophys. 89:230, 1960; Porter, Biochem. J. 73:119, 1959; Edelman et al., Methods in Enzymology, Vol. 1, page 422, Academic Press, 1967; and Coligan et al. at sections 2.8.1-2.8.10 and 2.10.1-2.10.4).

Other methods of cleaving antibodies, such as separation of heavy chains to form monovalent light-heavy chain fragments, further cleavage of fragments, or other enzymatic, chemical, or genetic techniques may also be used, so long as the fragments bind to the antigen that is recognized by the intact antibody.

One of skill will realize that conservative variants of the antibodies can be produced. Such conservative variants employed in antibody fragments, such as dsFv fragments or in scFv fragments, will retain critical amino acid residues necessary for correct folding and stabilizing between the V_(H) and the V_(L) regions, and will retain the charge characteristics of the residues in order to preserve the low pI and low toxicity of the molecules. Amino acid substitutions (such as at most one, at most two, at most three, at most four, or at most five amino acid substitutions) can be made in the V_(H) and the V_(L) regions to increase yield. Conservative amino acid substitution tables providing functionally similar amino acids are well known to one of ordinary skill in the art. The following six groups are examples of amino acids that are considered to be conservative substitutions for one another: 1) Alanine (A), Serine (S), Threonine (T); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

In some examples, naked antibodies can be administered at at least 5 mg per kg every two weeks, such as at least 10 mg per kg, at least 25 mg per kg, at least 30 mg per kg, at least 50 mg per kg (for example, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 mg per kg), at least once a week, at least once every 2 weeks, at least once every 3 weeks, or at least once every month depending upon the ovarian cancer. In an example, the antibodies are administered continuously. In another example, antibodies or antibody fragments conjugated to cytotoxic agents (immunotoxins) are administered at at least 10 μg per kg, such as at least 20, at least 30, at least 50, at least 70, at least 100 μg per kg, at least twice a week, at least once a week, at least once every two weeks, at least once every month depending upon the ovarian cancer. In one example, 50 μg per kg is administered twice a week for 2 to 3 weeks. In other examples, the subject is administered the therapeutic composition that a binding agent specific for one or more of the disclosed ovarian endothelial cell tumor-associated molecules daily for a period of at least 30 days, such as at least 2 months, at least 4 months, at least 6 months, at least 12 months, at least 24 months, or at least 36 months. Subjects can be monitored by methods known to those skilled in the art to determine ovarian tumor responsiveness to the antibody treatment. The subject can be monitored by non invasive techniques such as CT or MRI imaging to assess tumor response. It is contemplated that additional agents can be administered, such as antineoplastic agents in combination with or following treatment with the antibodies.

Methods of Evaluating the Effectiveness of an Ovarian Tumor Treatment

Methods are disclosed herein for determining the effectiveness of a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules) for the treatment of an ovarian tumor in a subject with the ovarian tumor. In an example, the method includes detecting expression of an ovarian endothelial cell tumor-associated molecule in a sample from the subject following administration of the binding agent (such as an siRNA), for example at least 24 hours, at least 1 week, at least 2 weeks, or at least 4 weeks following administration of the agent. The expression of the ovarian endothelial cell tumor-associated molecule following administration can be compared to a control, such as a reference value. An alteration in the expression of the ovarian endothelial cell tumor-associated molecule relative to the control following administration indicates that the agent is effective for the treatment of the ovarian cancer in the subject.

In a specific example, the method includes detecting and comparing the protein expression levels of the ovarian endothelial cell tumor-associated molecules. In other examples, the method includes detecting and comparing the mRNA expression levels of the ovarian endothelial cell tumor-associated molecules. In certain examples, the treatment is considered effective if the expression levels are altered by at least 2-fold, such as by at least 3-fold, at least 4-fold, at least 6-fold or at least 10-fold relative to the control.

In one example, the specific ovarian endothelial cell tumor-associated molecule is detected in a biological sample. In a particular example, the biological sample is a tumor biopsy. In another example, the ovarian endothelial cell tumor-associated molecule is detected in a serum sample. For example, the ovarian endothelial cell tumor-associated molecule is detected in a serum sample if the specific molecule is known to be secreted or located on a cell surface susceptible to enzymatic cleavage.

Altering Ovarian Endothelial Cell Tumor-Associated Molecules' Activity Such as Expression

In an example, an alteration in the expression of one or more of the disclosed ovarian endothelial cell tumor-associated molecules following administration includes an increase or decrease in production of a gene product/expression, such as RNA or protein. For example, an alteration can include processes that downregulate or decrease transcription of a gene or translation of mRNA whose expression or activity is increased in ovarian endothelial tumor cells. Gene downregulation includes any detectable decrease in the production of a gene product. In certain examples, production/expression of a gene product decreases by at least 2-fold, for example at least 3-fold, at least 4-fold, at least 6-fold, or at least 10-fold as compared to a control. Exemplary ovarian endothelial cell tumor-associated molecules that are up-regulated in ovarian tumor endothelial cells are presented in Tables 1, 2, 4 and 5. Thus, a decrease in the expression of one or more of the molecules listed in Tables 1, 2, 4 or 5 that is noted as being up-regulated in ovarian tumor endothelial cells following treatment indicates that the agent is of use for treating the ovarian cancer.

Exemplary ovarian endothelial cell tumor-associated molecules that are down-regulated in ovarian tumor endothelial cells are presented in Table 1 with specific examples provided in Table 3. Thus, an increase in the expression of one or more of the molecules listed in Table 3 following administration indicates that the agent is effective for the treatment of ovarian cancer.

In another example, an alteration can include processes that increase transcription of a gene or translation of mRNA. Gene up-regulation includes any detectable increase in the production of a gene product. In certain examples, production/expression of a gene product increases by at least 2-fold, for example at least 3-fold or at least 4-fold, at least 6-fold, at least 10-fold or at least 28-fold following treatment as compared to a control.

Detection of Ovarian Endothelial Cell Tumor-Associated Nucleic Acids

Nucleic acids can be detected by any method known in the art. In some examples, nucleic acids are isolated, amplified, or both, prior to detection. In an example, the biological sample can be incubated with primers that permit the amplification of one or more of the disclosed ovarian endothelial cell tumor-associated mRNAs, under conditions sufficient to permit amplification of such products. For example, the biological sample is incubated with probes that can bind to one or more of the disclosed ovarian endothelial cell tumor-associated nucleic acid sequences (such as cDNA, genomic DNA, or RNA (such as mRNA)) under high stringency conditions. The resulting hybridization can then be detected using methods known in the art. In one example, the effectiveness of an ovarian tumor treatment is identified by applying isolated nucleic acid molecules to an array in which the isolated nucleic acid molecules are obtained from a biological sample including ovarian endothelial cancer cells following treatment with the ovarian tumor treatment. In such example, the array includes oligonucleotides complementary to all ovarian endothelial cell tumor-associated genes listed in Table 1. In a particular example, the array is a commercially available array such as a U133 Plus 2.0 oligonucleotide array from AFFYMETRIX® (AFFYMETRIX®, Santa Clara, Calif.).

In an example, the isolated nucleic acid molecules are incubated with the array including oligonucleotides complementary to the ovarian endothelial cell tumor-associated molecules that are up-regulated in ovarian tumor endothelial cells, such as those listed in Table 2, Table 3, Table 4 and/or Table 5 for a time sufficient to allow hybridization between the isolated nucleic acid molecules and oligonucleotide probes, thereby forming isolated nucleic acid molecule:oligonucleotide complexes. The isolated nucleic acid molecule:oligonucleotide complexes are then analyzed to determine if expression of the isolated nucleic acid molecules is altered. In such example, an ovarian tumor treatment is effective if a decrease in the expression of ovarian endothelial tumor-associated molecules is observed as compared to a control (such as a normal endothelial cell) or reference value. In an additional example, the array includes oligonucleotides complementary to the ovarian endothelial cell tumor-associated molecules that down-regulated in ovarian tumor endothelial cells, such as those listed in Table 3. In this example, an ovarian tumor treatment is effective if an increase in the expression of one or more ovarian endothelial tumor-associated molecules is observed.

Gene Expression Profile

A gene expression profile is disclosed herein that can be used to identify the effectiveness of an ovarian tumor treatment. In an example, the gene expression profile includes at least two of the ovarian endothelial cell tumor-associated molecules listed in Table 1, such as at least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, or at least 1100 molecules (for example, 2, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 120, 130, 140, 150, 175, 225, 275, 325, 350, 375, 450, 550, 650, 750, 850, 950, 1050 or 1149 of those listed).

In a particular example, the gene expression profile includes at least 2, at least 5, at least 7, at least 10, at least 20, at least 25, at least 27 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 25, 26, 27, 28 or 29 molecules) listed in Table 2, Table 4 and/or Table 5 that are associated with an at least six-fold increase in expression in tumor endothelial cells. In a particular example, the at least two molecules include EGFL6 and TNFAIP6. In other particular examples, the at least two ovarian endothelial cell tumor-associated molecules include EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, and PLXDC1.

In other particular examples, the gene expression profile includes at least 2, at least 5, at least 7, at least 10, at least 13, or at least 15 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 molecules) that are down-regulated in ovarian tumor endothelial cells as listed in Table 3. For example, the profile includes the seventeen ovarian endothelial cell tumor-associated molecules listed in Table 3.

Detecting Ovarian Endothelial Cell Tumor-Associated Proteins

As an alternative to analyzing the sample for the presence of nucleic acids, the presence of proteins can be determined. Proteins can be detected by any method known in the art. In some examples, proteins are purified prior to detection. For example, the effect of an ovarian tumor treatment can be determined by incubating the biological sample with one or more antibodies that specifically binds to one of the disclosed ovarian endothelial cell tumor-associated proteins encoded by the genes listed in Tables 1, Table 2, Table 3, Table 4 or Table 5 to detect expression. The primary antibody can include a detectable label. For example, the primary antibody can be directly labeled, or the sample can be subsequently incubated with a secondary antibody that is labeled (for example with a fluorescent label). The label can then be detected, for example by microscopy, ELISA, flow cytometery, or spectrophotometry. In another example, the biological sample is analyzed by Western blotting for the presence or absence of the specific ovarian endothelial cell tumor-associated molecule. In other examples, the biological sample is analyzed by mass spectrometry for the presence or absence of the specific ovarian endothelial cell tumor-associated molecule.

In one example, the antibody that specifically binds an ovarian endothelial cell tumor-associated molecule (such as those listed in Table 1) is directly labeled with a detectable label. In another example, each antibody that specifically binds an ovarian endothelial cell tumor-associated molecule (the first antibody) is unlabeled and a second antibody or other molecule that can bind the human antibody that specifically binds the respective ovarian endothelial cell tumor-associated molecule is labeled. As is well known to one of skill in the art, a second antibody is chosen that is able to specifically bind the specific species and class of the first antibody. For example, if the first antibody is a human IgG, then the secondary antibody can be an anti-human-IgG. Other molecules that can bind to antibodies include, without limitation, Protein A and Protein G, both of which are available commercially.

Suitable labels for the antibody or secondary antibody include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, magnetic agents and radioactive materials. Non-limiting examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase. Non-limiting examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin. Non-limiting examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin. A non-limiting exemplary luminescent material is luminol; a non-limiting exemplary magnetic agent is gadolinium, and non-limiting exemplary radioactive labels include ¹²⁵I, ¹³¹I, ³⁵S or ³H.

In an alternative example, ovarian endothelial cell tumor-associated molecules can be assayed in a biological sample by a competition immunoassay utilizing ovarian endothelial cell tumor-associated molecule standards labeled with a detectable substance and unlabeled antibody that specifically bind to the desired ovarian endothelial cell tumor-associated molecule. In this assay, the biological sample (such as serum, tissue biopsy, or cells isolated from a tissue biopsy), the labeled ovarian endothelial cell tumor-associated molecule standards and the antibody that specifically binds to ovarian endothelial cell tumor-associated molecule are combined and the amount of labeled ovarian endothelial cell tumor-associated molecule standard bound to the unlabeled antibody is determined. The amount of ovarian endothelial cell tumor-associated molecule in the biological sample is inversely proportional to the amount of labeled ovarian endothelial cell tumor-associated molecule standard bound to the antibody that specifically binds the ovarian endothelial cell tumor-associated molecule.

Identifying Agents to Treat Ovarian Cancer

Methods are provided herein for identifying agents to treat an ovarian cancer. For example, agents that decrease expression or activity of a gene that is upregulated in ovarian endothelial tumor cells (such as those listed in Tables 2 and 4), as well as agents that increase activity of a gene that is downregulated in ovarian endothelial tumor cells (such as those listed in Table 3), can be identified using these methods. In an example, the method includes contacting an ovarian tumor endothelial cell with one or more test agents under conditions sufficient for the one or more test agents to alter the activity of at least one ovarian endothelial cell tumor-associated molecule listed in any of Tables 1-5. It is contemplated that several doses of the agent can be tested and then expression levels of nucleic acids or proteins can be determined. The method also includes detecting the activity or expression of the at least one ovarian endothelial cell tumor-associated molecule in the presence and absence of the one or more test agents. The activity or expression of the at least one ovarian endothelial cell tumor-associated molecule in the presence of the one or more test agents is then compared to the activity or expression of the at least one ovarian endothelial cell tumor-associated molecule in the absence of such agents to determine if there is differential expression of the at least one ovarian endothelial cell tumor associated molecule. In several examples, differential expression of the ovarian endothelial cell tumor-associated molecule in the presence of the agent (as compared to expression in the absence of the agent) indicates that the one or more test agents is of use to treat the ovarian tumor.

In an example, determining whether there is differential expression of one or more ovarian endothelial cell tumor-associated molecules includes generating a gene expression profile for the subject. For example, a gene expression profile for the subject can be generated by using an array of molecules including an ovarian endothelial cell tumor-associated expression profile.

Ovarian Endothelial Cell Tumor-Associated Molecules

Ovarian endothelial cell tumor-associated molecules can include nucleic acid sequences (such as DNA, cDNA, or mRNAs) and proteins. In a specific example, detecting differential expression of the ovarian endothelial cell tumor-associated molecules includes detecting differential mRNA expression of the disclosed ovarian endothelial cell tumor-associated molecules. For example, such differential expression can be measured by real time quantitative polymerase chain reaction or microarray analysis or other methods known in the art. In another example, detecting differential expression of the ovarian endothelial cell tumor-associated molecules includes detecting differential protein expression of the disclosed ovarian endothelial cell tumor-associated molecules. For example, protein differential expression is measured by Western blot analysis or a protein microarray.

Test Agents

The one or more test agents can be any substance, including, but not limited to, a protein (such as an antibody), a nucleic acid molecule (such as a siRNA), an organic compound, an inorganic compound, a small molecule or any other molecule of interest. In a particular example, the test agent is a siRNA that reduces or inhibits the activity (such as the expression) of one of the ovarian endothelial cell tumor-associated molecules listed in Tables 2, 4 or 5. For example, the siRNA is directed to an ovarian endothelial cell tumor-associated molecule listed in Table 2, 4 or 5 which is involved in angiogenesis, such as a molecule that is involved in at least one of cell proliferation, tube formation or cell motility.

In other examples, the test agent is an antibody. For example, the antibody is directed to specifically bind to an ovarian endothelial cell tumor-associated protein encoded by one of the genes listed in any of Tables 1, 2, 4 or 5 that are upregulated in ovarian endothelial tumor cells. In a particular example, the antibody is directed to an ovarian endothelial cell tumor-associated protein encoded by one of the genes listed in Tables 2, 4 or 5 that is upregulated in ovarian endothelial tumor cells and which is involved in angiogenesis, such as a gene that is involved in at least one of cell proliferation, tube formation or cell motility. In another example, the test agent is a nucleic acid encoding one or more of the proteins listed in Table 3. For example, the nucleic acid can be part of a vector suitable for gene therapy.

Altering Ovarian Endothelial Cell Tumor-Associated Molecules' Activity

In an example, an alteration in the activity of one or more of the disclosed ovarian endothelial cell tumor-associated molecules includes an increase or decrease in production of a gene product, such as RNA or protein. For example, an alteration can include processes that downregulate or decrease transcription of a gene or translation of mRNA. Gene downregulation includes any detectable decrease in the production of a gene product. In certain examples, production/expression of a gene product decreases by at least 2-fold, for example at least 3-fold, at least 4-fold, at least 6-fold, or at least 10-fold as compared to a control (such as a reference value or a normal endothelial cell). For example, a decrease in one or more of the disclosed ovarian endothelial cell tumor-associated molecules up-regulated in ovarian tumor endothelial cells (such as those listed in Tables 2,

4 and 5), is indicative of an agent that is effective at treating ovarian cancer.

In another example, an alteration can include processes that increase transcription of a gene or translation of mRNA. Gene up-regulation includes any detectable increase in the production of a gene product. In certain examples, production/expression of a gene product increases by at least 2-fold, for example at least 3-fold or at least 4-fold, at least 6-fold, at least 10-fold or at least 28-fold as compared to a control. For example, an increase in one or more of the disclosed ovarian endothelial cell tumor-associated molecules down-regulated in ovarian tumor endothelial cells (such as those listed in Table 3) is indicative of an agent that is effective at treating ovarian cancer.

Detection of Ovarian Endothelial Cell Tumor-Associated Nucleic Acids

Nucleic acids can be detected by any method known in the art, such as those described above. In one example, a therapeutic agent is identified by applying isolated nucleic acid molecules to an array in which the isolated nucleic acid molecules are obtained from a biological sample including ovarian endothelial cancer cells following treatment with the one or more test agents. In such example, the array includes oligonucleotides complementary to all ovarian endothelial cell tumor-associated genes listed in Table 1. In a particular example, the array is a commercially available array such as a U133 Plus 2.0 oligonucleotide array from AFFYMETRIX® (AFFYMETRIX®, Santa Clara, Calif.).

In an example, the isolated nucleic acid molecules are incubated with the array including oligonucleotides complementary to the ovarian endothelial cell tumor-associated molecules listed in Table 2, 4 and/or 5 for a time sufficient to allow hybridization between the isolated nucleic acid molecules and oligonucleotide probes, thereby forming isolated nucleic acid molecule:oligonucleotide complexes. The isolated nucleic acid molecule:oligonucleotide complexes are then analyzed to determine if expression of the isolated nucleic acid molecules is altered. In such example, an agent is considered is effective if the test agent decreases expression of ovarian endothelial tumor-associated molecules upregulated in ovarian endothelial cell tumors relative to the absence of the agent (such as a decrease of at least 2-, 3-, 4-, 5- or 10-fold). Similarly, an agent is considered is effective if the test agent increases expression of ovarian endothelial tumor-associated molecules downregulated in ovarian endothelial cell tumors relative to the absence of the agent (such as an increase of at least 2-, 3-, 4-, 5- or 10-fold).

Gene Expression Profile

The disclosed gene profile (as described above) can also be used to identify agents to treat an ovarian tumor, such as a cancer, in a subject. In an example, the gene expression profile includes at least two of the ovarian endothelial cell tumor-associated molecules listed in Table 1, such as at least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, or at least 1100 molecules (for example, 2, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 120, 130, 140, 150, 175, 225, 275, 325, 350, 375, 450, 550, 650, 750, 850, 950, 1050 or 1149 of those listed).

In a particular example, the gene expression profile includes at least 2, at least 5, at least 7, at least 10, at least 20, at least 25, or at least 27 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 25, 26, 27, 28 or 29 molecules) listed in Table 2, 4 and/or 5 that are associated with an at least six-fold increase in expression in tumor endothelial cells. In a particular example, the at least two molecules include EGFL6 and TNFAIP6. In other particular examples, the at least two ovarian endothelial cell tumor-associated molecules include EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, and PLXDC1.

In other particular examples, the gene expression profile includes at least 2, at least 5, at least 7, at least 10, at least 13, or at least 15 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 molecules) that are down-regulated in ovarian tumor endothelial cells as listed in Table 3. For example, the profile includes the seventeen ovarian endothelial cell tumor-associated molecules listed in Table 3.

Detecting Ovarian Endothelial Cell Tumor-Associated Proteins

As an alternative to analyzing the sample for the presence of nucleic acids, the presence of proteins can be determined using any method known in the art. In some examples, proteins are purified before detection. For example, the effect of one or more test agents on an ovarian tumor can be determined by incubating the biological sample with an antibody that specifically binds to one of the disclosed ovarian endothelial cell tumor-associated proteins encoded by the genes listed in Tables 1-5. The primary antibody can include a detectable label. For example, the primary antibody can be directly labeled, or the sample can be subsequently incubated with a secondary antibody that is labeled (for example with a fluorescent label). The label can then be detected, for example by microscopy, ELISA, flow cytometery, or spectrophotometry. In another example, the biological sample is analyzed by Western blotting for the presence or absence of the specific ovarian endothelial cell tumor-associated molecule. In some examples, the biological sample is analyzed by mass spectrometry.

In one example, the antibody that specifically binds an ovarian endothelial cell tumor-associated molecule (such as those listed in Table 1) is directly labeled with a detectable label. In another example, each antibody that specifically binds an ovarian endothelial cell tumor-associated molecule (the first antibody) is unlabeled and a second antibody or other molecule that can bind the human antibody that specifically binds the respective ovarian endothelial cell tumor-associated molecule is labeled. As is well known to one of skill in the art, a second antibody is chosen that is able to specifically bind the specific species and class of the first antibody. For example, if the first antibody is a human IgG, then the secondary antibody can be an anti-human-IgG. Other molecules that can bind to antibodies include, without limitation, Protein A and Protein G, both of which are available commercially.

Suitable labels for the antibody or secondary antibody include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, magnetic agents and radioactive materials. Non-limiting examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase. Non-limiting examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin. Non-limiting examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin. A non-limiting exemplary luminescent material is luminol; a non-limiting exemplary magnetic agent is gadolinium, and non-limiting exemplary radioactive labels include ¹²⁵I, ¹³¹I, ³⁵S or ³H.

In an alternative example, ovarian endothelial cell tumor-associated molecules can be assayed in a biological sample by a competition immunoassay utilizing ovarian endothelial cell tumor-associated molecule standards labeled with a detectable substance and an unlabeled antibody that specifically binds the desired ovarian endothelial cell tumor-associated molecule. In this assay, the biological sample (such as serum, tissue biopsy, or cells isolated from a tissue biopsy), the labeled ovarian endothelial cell tumor-associated molecule standards and the antibody that specifically binds the desired ovarian endothelial cell tumor-associated molecule are combined and the amount of labeled ovarian endothelial cell tumor-associated molecule standard bound to the unlabeled antibody is determined. The amount of ovarian endothelial cell tumor-associated molecule in the biological sample is inversely proportional to the amount of labeled ovarian endothelial cell tumor-associated molecule standard bound to the antibody that specifically binds the ovarian endothelial cell tumor-associated molecule.

Methods of Diagnosing and Prognosing an Ovarian Tumor

Metastasis is a major complication in the pathogenesis of tumors, such as ovarian cancer, and is typically indicative of poor prognosis. It is also known that angiogenesis is a crucial factor in the progression of solid tumors and metastases, including ovarian cancer. The formation of the vascular stroma plays an important role in the pathophysiology of malignancy. For instance, in the absence of vascular support tumors may become necrotic, or even apoptotic. In contrast, the onset of angiogenesis marks a phase of rapid proliferation, local invasion, and ultimately metastasis.

Without wishing to be bound to a particular theory, it is proposed that an alteration in the expression of the disclosed ovarian endothelial tumor-associated molecules associated with angiogenesis, such as molecules involved in cell proliferation, cell motility or tube formation, including those disclosed in FIG. 5 (such as EZH2), is related to enhanced ovarian tumor cell metastasis and a poor clinical outcome. Thus, methods of diagnosing or prognosing an ovarian tumor that overexpresses at least one pro-angiogenic ovarian endothelial cell tumor-associated molecule (such as those listed in Tables 1, 2, 4 and 5 that are upregulated in ovarian endothelial tumor cells; e.g., EZH2) or underexpresses at least one proangiogenic ovarian endothelial cell tumor associated molecule (such as those listed in Tables 1 and 3 that are downregulated in ovarian endothelial tumor cells), are disclosed. In some examples, such methods can be used to identify those subjects that will benefit from the disclosed treatment methods. For example, such diagnostic methods can be performed prior to the subject undergoing the treatments described above. In other examples, these methods are utilized to predict the metastatic potential of the ovarian cancer, a poor prognosis, or combinations thereof. In one particular example, these methods are utilized to predict a poor prognosis, such as to indicate a decreased survival time.

In an example, the method includes detecting expression of at least one angiogenic ovarian endothelial cell tumor-associated molecule listed in Tables 1-5, such as at least two, at least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200 ovarian endothelial cell tumor-associated molecules related to angiogenesis (for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 17, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 100, 125, 150, 175, 200, or 250 listed in Tables 1-5) in a sample from the subject exhibiting one or more symptoms associated with ovarian cancer.

In an example, the specific angiogenic ovarian endothelial cell tumor-associated molecule, such as EZH2, is detected in a biological sample. In a particular example, the biological sample is a sample taken from a subject with ovarian epithelial cancer. In a particular example, the biological sample is a tumor biopsy. In another example, the angiogenic ovarian endothelial cell tumor-associated molecule is detected in a serum sample. For example, the ovarian endothelial cell tumor-associated molecule is detected in a serum sample if the specific molecule is secreted or located on a cell surface susceptible to enzymatic cleavage.

In one example, detection of at least one angiogenic ovarian endothelial cell tumor-associated molecule listed in any of Tables 1, 2, 3, 4 or 5, such as detection of EZH2, in a biological sample from the subject is used to diagnose or prognose an ovarian tumor. Methods of detecting such molecules in a sample are known in the art and are routine. In some examples, the relative amount of pro-angiogenic ovarian endothelial cell tumor-associated molecules present is determined, for example by quantitating the expression level of such molecules. For example, the relative or absolute quantity of the at least one angiogenic ovarian endothelial cell tumor-associated molecule in a sample can be determined.

The activity such as the expression level of the disclosed pro-angiogenic ovarian endothelial cell tumor-associated molecules in a sample obtained from a subject is compared to a control. In one example, an increase in expression of one or more of the angiogenic ovarian endothelial cell tumor-associated molecules upregulated in ovarian tumor endothelial cells (such as those listed in Table 2) as compared to a non-tumor control or reference value indicates the presence of an ovarian tumor, the ovarian tumor is metastatic, the ovarian tumor is likely to become metastatic, a poor prognosis or a combination thereof. In some examples, a decrease in expression of one or more of the angiogenic ovarian endothelial cell tumor-associated molecules that is downregulated in ovarian tumor endothelial cells (such as those listed in Table 3 or VASH1) as compared to a non-tumor control or reference value indicates the presence of an ovarian tumor, the ovarian tumor is metastatic, the ovarian tumor is likely to become metastatic, a poor prognosis or a combination thereof.

For example, the level of the angiogenic ovarian endothelial cell tumor-associated molecules, such as the level of EZH2, detected can be compared to a non-tumor control or reference value, such as a value that represents a level of angiogenic ovarian endothelial cell tumor-associated molecules expected if an ovarian tumor is or is not metastatic or is a low grade tumor or early stage tumor. In one example, the angiogenic ovarian endothelial cell tumor-associated molecules detected in a tumor sample are compared to the level of such molecules detected in a sample obtained from a subject that does not have an ovarian tumor or has a non-metastatic ovarian tumor. In certain examples, detection of at least a 2-fold, such as by at least 3-fold, at least 4-fold, at least 6-fold or at least 10-fold alteration in the relative amount of the pro-angiogenic ovarian endothelial cell tumor-associated molecules in a tumor sample, as compared to the relative amount of such molecules in a control indicates that the subject has a tumor with metastatic potential, has a tumor that has metastasized, has a poor prognosis, or combinations thereof. In some examples, detection of statistically similar relative amounts of pro-angiogenic ovarian endothelial cell tumor-associated molecules observed in a tumor sample, as compared to the relative amount of such molecules in a control sample that is not metastatic, indicates that that subject does not have a tumor with metastatic potential, does not have a tumor that has metastasized, has a good prognosis, or combinations thereof.

In a specific example, the method includes detecting and comparing the nucleic acid expression levels of the pro-angiogenic ovarian endothelial cell tumor-associated molecules such as DNA, cDNA, or mRNAs. In a specific example, the method includes detecting and comparing the mRNA expression levels of the pro-angiogenic ovarian endothelial cell tumor-associated molecules. For example, such expression can be measured by real time quantitative polymerase chain reaction or microarray analysis. In a particular example, the disclosed gene expression profile is utilized to diagnosis and/or prognosis an ovarian tumor.

Detection of Ovarian Endothelial Cell Tumor-Associated Nucleic Acids

Nucleic acids can be detected by any method known in the art. In some examples, nucleic acids are isolated, amplified, or both, prior to detection. In an example, the biological sample can be incubated with primers that permit the amplification of one or more of the disclosed ovarian endothelial cell tumor-associated mRNAs, under conditions sufficient to permit amplification of such products. For example, the biological sample is incubated with probes that can bind to one or more of the disclosed ovarian endothelial cell tumor-associated nucleic acid sequences (such as cDNA, genomic DNA, or RNA (such as mRNA)) under high stringency conditions. The resulting hybridization can then be detected using methods known in the art. In one example, a therapeutic agent is identified by applying isolated nucleic acid molecules to an array in which the isolated nucleic acid molecules are obtained from a biological sample including ovarian endothelial cancer cells for example following treatment with the one or more test agents. In such example, the array includes oligonucleotides complementary to all ovarian endothelial cell tumor-associated genes listed in Table 1. In a particular example, the array is a commercially available array such as a U133 Plus 2.0 oligonucleotide array from AFFYMETRIX® (AFFYMETRIX®, Santa Clara, Calif.).

In an example, the isolated nucleic acid molecules are incubated with the array including oligonucleotides complementary to the ovarian endothelial cell tumor-associated molecules listed in Tables 2, 3, 4 and/or 5 for a time sufficient to allow hybridization between the isolated nucleic acid molecules and oligonucleotide probes, thereby forming isolated nucleic acid molecule:oligonucleotide complexes. In a particular example, the isolated nucleic acid molecules are incubated with the array including oligonucleotides complementary to at least EZH2. The isolated nucleic acid molecule:oligonucleotide complexes are then analyzed to determine if expression of the isolated nucleic acid molecules is altered.

Gene Expression Profile

The disclosed gene profile (as described above) can also be used in the diagnosis and prognosis of an ovarian tumor in a subject. In an example, the gene expression profile includes at least two of the ovarian endothelial cell tumor-associated molecules listed in Table 1, such as at least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, or at least 1100 molecules (for example, 2, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 120, 130, 140, 150, 175, 225, 275, 325, 350, 375, 450, 550, 650, 750, 850, 950, 1050 or 1149 of those listed).

In a particular example, the gene expression profile includes at least 1, at least 3, at least 5, at least 7, at least 10, at least 20, at least 25, or at least 27 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 25, 26, 27, 28 or 29 molecules) listed in Table 2, 4 and/or 5 that are associated with angiogenesis, such as molecules involved in cell proliferation, cell motility and/or tube formation. In a particular example, the at least one molecule includes EZH2.

In other particular examples, the gene expression profile includes at least 2, at least 5, at least 7, at least 10, at least 13, or at least 15 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 molecules) that are down-regulated in ovarian tumor endothelial cells as listed in Table 3. For example, the profile includes the seventeen ovarian endothelial cell tumor-associated molecules listed in Table 3.

Detecting Ovarian Endothelial Cell Tumor-Associated Proteins

As an alternative to analyzing the sample for the presence of nucleic acids, alterations in protein expression can be measured by methods known in the art such as Western blot analysis, mass spectrometry, immunoassay or a protein microarray (as described above). For example, the metastatic potential of an ovarian tumor can be determined by using a protein array that includes one or more capture agents, such as antibodies that are specific for the one or more disclosed ovarian endothelial tumor-associated molecules that are related to angiogenesis, such as molecules that play a role in cell proliferation, cell motility or tube formation, such as EZH2.

The disclosure is further illustrated by the following non-limiting Examples.

Example 1 Materials and Methods for Examples 2-7 Sample Preparation.

Fresh tissue samples (5 normal ovaries and 10 epithelial high-grade, stage III or IV invasive serous ovarian cancers) were obtained from patients undergoing primary surgical exploration at the M.D. Anderson Cancer Center. The minced tissue was digested with collagenase A, elastase and DNase 1 at 37° C. for 90 minutes to yield a single cell suspension. A number of negative selections followed including removal of platelets and red blood cells (RBCs) by Percoll separation, removal of epithelial cells using M450 beads, which are prebound to BerEP4 antibody, removal of leukocytes using anti-CD-14, CD-45, and CD-64 beads (Dynal Biotech, Brown Deer, Wis.). Positive selection was performed with P1H12 (CD 146) immunobeads (P1H12 antibody was from Chemicon, Temecula, Calif.), and the beads linked to secondary antibody were from Dynal Biotech. Immunostaining was then performed using von Willebrand factor and 4′,6-diamidino-2-phenylindole nuclear staining to confirm the purification of endothelial cells.

Total RNA Amplification for AFFYMETRIX° GENECHIP® Hybridization and Image Acquisition.

To successfully generate sufficient labeled cRNA for microarray analysis from 25 ng of total RNA, two rounds of amplification were necessary. For the first round synthesis of double-stranded cDNA, 25 ng of total RNA was reverse transcribed using the Two-Cycle cDNA Synthesis Kit (AFFYMETRIX®, Santa Clara, Calif.) and oligo-dT24-T7 (SEQ ID NO:1: 5′-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-3′) primer according to the manufacturer's instructions followed by amplification with the MEGA script T7 Kit (Ambion, Inc., Austin, Tex.). After cleanup of the cRNA with a GENECHIP® Sample Cleanup Module IVT column (AFFYMETRIX®), second round double stranded cDNA was amplified using the IVT Labeling Kit (AFFYMETRIX®). A 15.0 μg aliquot of labeled product was fragmented by heat and ion-mediated hydrolysis at 94° C. for 35 minutes in 24 μl H₂O and 6 μl of 5× Fragmentation Buffer (AFFYMETRIX®). The fragmented cRNA was hybridized for 16 hr at 45° C. in a Hybridization Oven 640 to a U133 plus 2.0 oligonucleotide array (AFFYMETRIX®). Washing and staining of the arrays with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, Oreg.) was completed in a Fluidics Station 450 (AFFYMETRIX®). The arrays were then scanned using a confocal laser GENECHIP® Scanner 3000 and GENECHIP® Operating Software (AFFYMETRIX®).

Data Normalization and Filtering.

Global normalization at a target value of 500 was applied to all 15 of the arrays under consideration using GENECHIP® Operating Software (AFFYMETRIX®). Normalized data were uploaded into the National Cancer Institute's Microarray Analysis Database (mAdb) for quality control screening and collation prior to downstream analyses. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data. BRB-ArrayTools is a multifunctional Excel add-in that contains utilities for processing and analyzing microarray data using the R version 2.0.1 environment (R Development Core Team, 2004). Of the 47,000 transcripts represented on the array, hybridization control probe sets and probe sets scored as absent at α1=0.05 or marginal (M) at α2=0.065 were excluded. In addition, only those transcripts present in greater than 50% of the arrays and displaying a variance in the top 50th percentile were evaluated.

Class Comparison Analysis.

Differentially expressed genes were identified for tumor and normal endothelial cell specimens using a multivariate permutation test in BRB-ArrayTools (Simon et al., “Design and Analysis of DNA Microarray Investigations” Springer-Verlag, 2003). A total of 2000 permutations were completed to identify the list of probe sets with a false discovery rate less than 10% at a confidence of 95%. Differential expression was considered significant at a p<0.001. A random-variance t-test was selected to permit the sharing of information among probe sets within class variation without assuming that all of the probe sets possess the same variance (Wright et al., Bioinformatics 19: 2448-2455, 2003). A global assessment of whether expression profiles were different between classes was also performed. During each permutation the class labels were reassigned randomly and the p-value for each probe set recalculated. The proportion of permutations yielding at least as many significant genes as the actual data set at a p-value<0.001 was reported as the significance level of the global test.

Pathway Analysis.

Differentially regulated genes identified in a series of 48 late-stage (III and IV) high-grade (Hurwitz et al., N. Engl. J. Med. 350: 2335-2342, 2004) microdissected papillary serous ovarian carcinomas, as compared to 10 normal ovarian surface epithelial brushings (Bonome et al., Cancer Res. 65: 10602-10612, 2005), were categorized by cellular component according to the Gene Ontology (GO) ontological hierarchy. Epithelial genes associated with the cell membrane, extracellular matrix, and extracellular region were used as central nodes to identify signaling pathways modulated in tumor-associated endothelial cell isolates. This was accomplished using PathwayAssist version 3.0 software (Iobion Informatics LLC, La Jolla, Calif.). This software package contains over 500,000 documented protein interactions acquired from MedLine using the natural language processing algorithm MEDSCAN. The proprietary database can be used to develop a biological association network (BAN) to identify putative co-regulated signaling pathways using expression data.

qRT-PCR Validation.

Quantitative real-time PCR (qRT-PCR) was performed on 100 ng of double-amplified product from the 15 specimens using primer sets specific for 23 select genes, and the housekeeping genes GAPDH, GUSB, and cyclophilin. An iCycler iQ Real-Time PCR Detection System (BIORAD® Laboratories, Hercules, Calif.) was used in conjunction with the QuantiTect SYBR Green RT-PCR Kit (QIAGEN® Inc., Valencia, Calif.) according to previously described cycling conditions (Donninger et al., Oncogene 23: 8065-8077, 2004). To calculate the relative expression for each gene, the 2-^(ΔΔC) _(T) method was used averaging the C_(T) values for the three housekeeping genes for a single reference gene value (Livak and Schmittgen, Methods 25: 402-408, 2001).

Immunohistochemical Staining.

Paraffin sections were stained for the following antibodies: rabbit anti-Fyn at 1:400 (Santa Cruz Biotechnology, Inc., Santa Cruz, Calif.), or rabbit anti-Fak at 1:50, mouse anti-MMP-9 at 1:40 (Oncogene-Research Products, Boston, Mass.), anti-β2-Arrestin at 1:200 (Santa Cruz Biotechnology, Inc.), anti-PLXDC1 at 1:200 (Abcam, Inc., Cambridge, Mass.), or anti-Jagged1 at 1:200 (Santa Cruz Biotechnology, Inc.) diluted in PBS at 4° C. After three washes in PBS, sections were incubated with secondary antibody for 1 hr at room temperature. Positive reactions were rendered visible by incubating the slides with stable 3,3-diaminobenzidine for 5-10 min. The sections were rinsed with distilled water, counterstained with Gill's hematoxylin for 30 s, and mounted with Universal Mount (Research Genetics, Huntsville, Ala.). The intensity of protein expression in the endothelial cells was evaluated using OPTIMAS 6.5 software and the mean optical density (OD) was calculated from 5 normal ovarian and 5 ovarian cancer samples. Ten vessels were selected randomly from each sample for the measurements.

Small Interfering RNA (siRNA).

The small interfering RNA (siRNA) constructs were purchased from QIAGEN® (Germantown, Md.): a control sequence with no homology to any human mRNA (as determined by BLAST search), and separate sequences designed to target EZH2, Jagged1, or PTK2 mRNA. The Jagged1 siRNA target sequence is SEQ ID NO: 2 (5′-CTGCATTTAGGGAGTATTCTA-3′). The EZH2 siRNA was targeted to the region corresponding to residues 85-106 of human EZH2 (Gene accession No. NM004456; 5′-AACCATGTTTACAACTATCAA-3′; SEQ ID NO: 3). The EZH2 siRNA sense sequence was 5′-CCAUGUUUACAACUAUCAAtt-3′; SEQ ID NO: 4) and the antisense sequence was 3′-ttGGUACAAAUGUUGAUAGUU-5′; SEQ ID NO: 5). For in vitro delivery, siRNA (5 μg) was incubated with 30 μL RNAiFect transfection reagent (QIAGEN®) for 10 min at room temperature and added to cells in culture at 80% confluence in 35 mm culture plates.

Cell Migration Assay.

Unstimulated motility was determined in membrane invasion culture system chambers containing polycarbonate filter (with 10 μm pores) that had been soaked in 0.1% gelatin, as described previously (Sood et al., Am. J. Pathol. 165: 1087-1095, 2004). HUVECs (1×105) were seeded in each upper well, allowed to incubate at 37° C. for 6 hr in Dulbecco's modified Eagle's medium (DMEM) containing 15% serum, and subsequently processed as described for the invasion assay.

Tube Formation Assay.

Matrigel (12.5 mg/ml) was thawed at 4° C. and 50 μl were quickly added to each well of a 96-well plate and allowed to solidify for 10 min at 37° C. The wells were then incubated for 6 h at 37° C. with HUVECs (20,000 cells/well), which had previously been treated for 18 h with the indicated siRNA. The formation of capillary-like structures was examined microscopically and photographs (50×) were taken using a RETIGA® 1300 camera and a ZEISS® Axiovert S100 microscope. The extent to which capillary-like structures formed in the gel was quantified by analysis of digitized images to determine the thread length of the capillary-like network, using a commercially available image analysis program (Northern Eclipse, North Tonawanda, N.Y.).

Example 2 Purity of Isolated Endothelial Cells

This example illustrates the purity of the endothelial cell samples utilized in the disclosed microarray analyses.

According to the methods described in Example 1, samples were immunostained with endothelial cell markers P1H12 and von Willebrand factor to determine endothelial cell purity. Immunostaining revealed that the employed purification technique yielded endothelial cell purity of >95% in all samples. Thus, the disclosed isolation technique resulted in a highly pure population of endothelial cells.

Example 3 Development of Gene Expression Profile for Ovarian Tumor-Endothelial Cells

This example provides a gene expression profile for ovarian tumor endothelial cells.

According to the methods described in Example 1, gene expression differences in purified endothelial cells from 10 invasive epithelial ovarian cancers and 5 normal (non-tumor) ovaries were determined by using the AFFYMETRIX® Human U133 Plus 2.0 Gene Chip platform. The nucleic acid sequence of each AFFYMETRIX® probe listed in the tables below is herein incorporated by reference, and is available from the AFFYMETRIX®website. As illustrated in Table 1, 1149 genes were identified as being differentially regulated ≧2-fold in endothelium derived from epithelial ovarian cancers compared to normal ovarian tissue. A positive fold change indicates the gene was upregulated in ovarian endothelial tumor sample and a negative fold change indicates the gene was downregulated in such sample. A multivariate permutation t-test (p<0.001) providing 95% confidence that the number of false discoveries did not exceed 10% of the complete gene list identified. In addition, global analysis of the gene list returned a p value<5×10⁻⁴.

TABLE 1 Gene expression profile. Affymetrix Parametric Fold Change Probe Set P-Value (Tumor/Normal) Gene Symbol Description Map 117_at 0.0005215 4.4 HSPA6 heat shock 70 kDa protein 6 1q23 (HSP70B′) (HSPA6), mRNA. 1552365_at 0.0008711 6.6 SCIN scinderin (SCIN), mRNA. 7p21.3 1552767_a_at 0.0002277 −6.5 HS6ST2 heparan sulfate 6-O- Xq26.2 sulfotransferase 2 (HS6ST2), mRNA. 1552790_a_at 0.0009635 −2.2 TLOC1 translocation protein 1 3q26.2 (TLOC1), mRNA. 1552889_a_at 0.0003238 2.5 XTP7 protein 7 transactivated by 19q13.32 hepatitis B virus X antigen (HBxAg) (XTP7), mRNA. 1553185_at 0.000128 4.6 RASEF RAS and EF-hand domain 9q21.32 containing 1553186_x_at 3.33E−05 5.3 RASEF RAS and EF-hand domain 9q21.32 containing 1553407_at 0.0003912 2.5 MACF1 Glycine-rich protein (GRP3S) 1p32-p31 1553538_s_at 0.000594 2.2 Unknown 1553569_at 0.0001391 2.6 Unknown 1553570_x_at 0.0002337 2.5 Unknown 1553575_at 2.80E−06 4.6 Unknown 1553909_x_at 0.0005681 3.8 C10orf6 Chromosome 10 open reading 10q24.32 frame 6 1553959_a_at 0.0009778 2.3 B3GALT6 UDP-Gal:betaGal beta 1,3- 1p36.33 galactosyltransferase polypeptide 6 (B3GALT6), mRNA. 1553983_at 0.000152 2.5 DTYMK deoxythymidylate kinase 2q37.3 (thymidylate kinase) (DTYMK), mRNA. 1554168_a_at 0.0003894 2.1 SH3KBP1 SH3-domain kinase binding Xp22.1-p21.3 protein 1 (SH3KBP1), transcript variant 2, mRNA. 1554309_at 0.0006114 2.3 EIF4G3 Eukaryotic translation initiation 1p36.12 factor 4 gamma, 3 1554334_a_at 7.15E−05 5.2 DNAJA4 DnaJ (Hsp40) homolog, 15q25.1 subfamily A, member 4 (DNAJA4), mRNA. 1554455_at 0.0007696 2.4 LINS1 lines homolog 1 (Drosophila) 15q26.3 (LINS1), transcript variant 2, mRNA. 1554464_a_at 0.000263 −2.8 CRTAP cartilage associated protein 3p22.3 (CRTAP), mRNA. 1554595_at 0.0005225 2.6 SYMPK Symplekin 19q13.3 1554640_at 0.0004537 2.6 PALM2-AKAP2 Paralemmin 2 9q31-q33 1554678_s_at 0.0002435 −2 HNRPDL Heterogeneous nuclear 4q13-q21 ribonucleoprotein D-like 1554703_at 0.0008778 2.1 ARHGEF10 Rho guanine nucleotide 8p23 exchange factor (GEF) 10 1555014_x_at 0.0004322 3.5 OK/SW-cl.92 1555241_at 0.0001337 3.2 Hypothetical gene supported by 8q21.2 BC055092 1555243_x_at 0.0001753 2.8 Hypothetical gene supported by 8q21.2 BC055092 1555374_at 0.0003108 4 TTL Tubulin tyrosine ligase 2q13 1555823_at 0.0001833 −2 BS 3076 14 1556126_s_at 1.04E−05 3.5 GPATC2 G patch domain containing 2 1q41 1556138_a_at 0.0001589 2.9 COL5A1 Collagen, type V, alpha 1 9q34.2-q34.3 1556185_a_at 0.0002463 2.6 CDNA clone IMAGE: 5260162 7 1556242_a_at 3.82E−05 2.1 Homo sapiens, clone 8 IMAGE: 3885623, mRNA 1556316_s_at 0.0005561 3.3 MIF Macrophage migration 22q11.23 inhibitory factor (glycosylation- inhibiting factor) 1556499_s_at 0.0005246 2.5 COL1A1 collagen, type I, alpha 1 17q21.3-q22.1 (COL1A1), mRNA. 1556835_s_at 0.0002018 2.2 Transcribed locus 11 1557432_at 0.0001321 3.6 RASAL2 RAS protein activator like 2 1q24 1557527_at 0.0003572 2.5 RUNX1 Runt-related transcription factor 21q22.3 1 (acute myeloid leukemia 1; aml1 oncogene) 1558019_at 2.09E−05 −2.9 DST Dystonin 6p12-p11 1558048_x_at 2.01E−05 4.1 Unknown 1558292_s_at 0.0007105 2 PIGW phosphatidylinositol glycan, 17q12 class W (PIGW), mRNA. 1558426_x_at 0.000189 2.9 Chromosome 7 open reading 7 frame 19 1558487_a_at 0.0002657 −2.6 TMED4 Transmembrane emp24 protein 7p13 transport domain containing 4 1558836_at 5.35E−05 3.2 MRNA; cDNA 2 DKFZp667A182 (from clone DKFZp667A182) 1559060_a_at 5.16E−05 3 KIAA1961 KIAA1961 gene 5q23.3 1559078_at 6.58E−05 4.6 BCL11A B-cell CLL/lymphoma 11A 2p16.1 (zinc finger protein) 1559101_at 9.12E−05 2.6 FYN FYN oncogene related to SRC, 6q21 FGR, YES 1559410_at 4.66E−05 3.6 Unknown 1559436_x_at 4.54E−05 4.8 ARRB2 Arrestin, beta 2 17p13 1559585_at 0.000489 3.2 FLJ31033 Hypothetical protein FLJ31033 4q32.3 1559593_a_at 0.0005238 2.9 CRSP7 Cofactor required for Sp1 19p13.11 transcriptional activation, subunit 7, 70 kDa 1560817_at 0.0001564 2.5 MOV10 Mov10, Moloney leukemia virus 1p13.2 10, homolog (mouse) 1562062_at 0.000114 4 Homo sapiens transcribed sequence with weak similarity to protein ref: NP_055301.1 (H. sapiens) neuronal thread protein [Homo sapiens] 1562063_x_at 0.0003481 3.4 Homo sapiens transcribed sequence with weak similarity to protein ref: NP_055301.1 (H. sapiens) neuronal thread protein [Homo sapiens] 1562270_at 0.000382 4 ARHGEF7 Rho guanine nucleotide 13q34 exchange factor (GEF) 7 1562271_x_at 1.81E−05 3.9 ARHGEF7 Rho guanine nucleotide 13q34 exchange factor (GEF) 7 1562456_at 0.0008617 2.3 MRNA; cDNA 11 DKFZp566C0924 (from clone DKFZp566C0924) 1563357_at 0.0002718 3.4 SERPINB9 serpin peptidase inhibitor, clade 6p25 B (ovalbumin), member 9 (SERPINB9), mRNA. 1565579_at 0.0003108 3.7 TATDN2 TatD DNase domain containing 2 3p25.3 1565823_at 1.91E−05 4.8 7-Sep septin 7 (SEPT7), transcript 7p14.3-p14.1 variant 2, mRNA. 1565974_at 0.0008723 2.8 SUV420H1 Suppressor of variegation 4-20 11q13.2 homolog 1 (Drosophila) 1566887_x_at 8.32E−05 4.3 KIAA0284 KIAA0284 14q32.33 1568619_s_at 0.0002665 2.2 LOC162073 Hypothetical protein 16p12.3 LOC162073 1568954_s_at 0.0001751 2.2 Unknown 1569519_at 0.0006199 2.5 FLJ21272 hypothetical protein FLJ21272 1q21.2 1569872_a_at 0.0004892 2.4 Homo sapiens, clone 16 IMAGE: 5242623 1570061_at 8.83E−05 3.2 CDNA clone IMAGE: 4555030 3 1570143_at 0.0005727 2.4 Homo sapiens, clone 8 IMAGE: 3932570, mRNA 1570185_at 0.0003081 3 Homo sapiens, clone 10 IMAGE: 5766850, mRNA 200005_at 0.0005509 −2 EIF3S7 eukaryotic translation initiation 22q13.1 factor 3, subunit 7 zeta, 66/67 kDa (EIF3S7), mRNA. 200010_at 0.0001997 −2.2 RPL11 Ribosomal protein L11 1p36.1-p35 200013_at 2.50E−05 −2.6 RPL24 ribosomal protein L24 (RPL24), 3q12 mRNA. 200021_at 0.0001035 2.5 CFL1 cofilin 1 (non-muscle) (CFL1), 11q13 mRNA. 200022_at 0.0002003 −2.1 RPL18 ribosomal protein L18 (RPL18), 19q13 mRNA. 200023_s_at 1.61E−05 −2.4 EIF3S5 eukaryotic translation initiation 11p15.4 factor 3, subunit 5 epsilon, 47 kDa (EIF3S5), mRNA. 200024_at 0.0004964 −2.5 RPS5 ribosomal protein S5 (RPS5), 19q13.4 mRNA. 200074_s_at 0.0001721 −2.2 RPL14 ribosomal protein L14 (RPL14), 3p22-p21.2 mRNA. 200081_s_at 6.20E−06 −3.3 RPS6 ribosomal protein S6 (RPS6), 9p21 mRNA. 200642_at 0.0007047 −2 SOD1 superoxide dismutase 1, soluble 21q22.11 (amyotrophic lateral sclerosis 1 (adult)) (SOD1), mRNA. 200651_at 0.0001597 −2.3 GNB2L1 guanine nucleotide binding 5q35.3 protein (G protein), beta polypeptide 2-like 1 (GNB2L1), mRNA. 200665_s_at 0.00039 2.7 SPARC secreted protein, acidic, 5q31.3-q32 cysteine-rich (osteonectin) (SPARC), mRNA. 200676_s_at 0.0007037 −2.5 UBE2L3 ubiquitin-conjugating enzyme 22q11.21 E2L 3 (UBE2L3), transcript variant 1, mRNA. 200700_s_at 4.15E−05 2.3 KDELR2 KDEL (Lys-Asp-Glu-Leu) 7p22.1 endoplasmic reticulum protein retention receptor 2 (KDELR2), mRNA. 200734_s_at 6.61E−05 2.5 ARF3 ADP-ribosylation factor 3 12q13 (ARF3), mRNA. 200735_x_at 9.63E−05 −2.1 NACA nascent-polypeptide-associated 12q23-q24.1 complex alpha polypeptide (NACA), mRNA. 200755_s_at 0.0007055 2.1 CALU calumenin (CALU), mRNA. 7q32 200760_s_at 5.53E−05 −2.6 ARL6IP5 ADP-ribosylation-like factor 6 3p14 interacting protein 5 (ARL6IP5), mRNA. 200806_s_at 0.0008155 −2 HSPD1 heat shock 60 kDa protein 1 2q33.1 (chaperonin) (HSPD1), nuclear gene encoding mitochondrial protein, transcript variant 2, mRNA. 200811_at 1.25E−05 −3.6 CIRBP cold inducible RNA binding 19p13.3 protein (CIRBP), mRNA. 200827_at 0.0004906 2.3 PLOD1 procollagen-lysine 1,2- 1p36.3-p36.2 oxoglutarate 5-dioxygenase 1 (PLOD1), mRNA. 200866_s_at 0.0004451 −2.1 PSAP prosaposin (variant Gaucher 10q21-q22 disease and variant metachromatic leukodystrophy) (PSAP), mRNA. 200883_at 7.19E−05 −3.2 UQCRC2 ubiquinol-cytochrome c 16p12 reductase core protein II (UQCRC2), mRNA. 200906_s_at 0.0002674 −3.2 KIAA0992 palladin (KIAA0992), mRNA. 4q32.3 200920_s_at 0.0001341 −2.3 BTG1 B-cell translocation gene 1, anti- 12q22 proliferative (BTG1), mRNA. 200937_s_at 5.83E−05 −2.4 RPL5 ribosomal protein L5 (RPL5), 1p22.1 mRNA. 200951_s_at 0.000314 4.1 CCND2 cyclin D2 (CCND2), mRNA. 12p13 200953_s_at 0.0001997 2.6 CCND2 cyclin D2 (CCND2), mRNA. 12p13 200965_s_at 0.000112 −5.9 ABLIM1 actin binding LIM protein 1 10q25 (ABLIM1), transcript variant 4, mRNA. 200999_s_at 0.0009198 2 CKAP4 cytoskeleton-associated protein 12q23.3 4 (CKAP4), mRNA. 201008_s_at 0.0009045 −2.7 TXNIP thioredoxin interacting protein 1q21.1 (TXNIP), mRNA. 201009_s_at 0.0004645 −2.8 TXNIP thioredoxin interacting protein 1q21.1 (TXNIP), mRNA. 201018_at 0.0007096 −2.3 EIF1AX eukaryotic translation initiation Xp22.12 factor 1A, X-linked (EIF1AX), mRNA. 201023_at 2.69E−05 −2.4 TAF7 TAF7 RNA polymerase II, 5q31 TATA box binding protein (TBP)-associated factor, 55 kDa (TAF7), mRNA. 201030_x_at 2.40E−05 −2.2 LDHB lactate dehydrogenase B 12p12.2-p12.1 (LDHB), mRNA. 201036_s_at 0.0005734 −3.7 HADHSC L-3-hydroxyacyl-Coenzyme A 4q22-q26 dehydrogenase, short chain (HADHSC), mRNA. 201054_at 1.41E−05 −2.2 HNRPA0 heterogeneous nuclear 5q31 ribonucleoprotein A0 (HNRPA0), mRNA. 201076_at 1.82E−05 −2.4 NHP2L1 NHP2 non-histone chromosome 22q13.2-q13.31 protein 2-like 1 (S. cerevisiae) (NHP2L1), transcript variant 2, mRNA. 201085_s_at 0.000222 −2.3 SON SON DNA binding protein 21q22.11 (SON), transcript variant a, mRNA. 201088_at 9.10E−06 2.7 KPNA2 karyopherin alpha 2 (RAG 17q23.1-q23.3 cohort 1, importin alpha 1) (KPNA2), mRNA. 201101_s_at 3.64E−05 −2.9 BCLAF1 BCL2-associated transcription 6q22-q23 factor 1 (BCLAF1), mRNA. 201129_at 0.0002614 −2.6 SFRS7 splicing factor, arginine/serine- 2p22.1 rich 7, 35 kDa (SFRS7), transcript variant 1, mRNA. 201133_s_at 0.0001686 −2.5 PJA2 praja 2, RING-H2 motif 5q21.3 containing (PJA2), mRNA. 201154_x_at 0.0001159 −2.2 RPL4 ribosomal protein L4 (RPL4), 15q22 mRNA. 201163_s_at 0.0003882 2.2 IGFBP7 insulin-like growth factor 4q12 binding protein 7 (IGFBP7), mRNA. 201193_at 0.0004945 −2.9 IDH1 isocitrate dehydrogenase 1 2q33.3 (NADP+), soluble (IDH1), mRNA. 201204_s_at 1.43E−05 2.2 RRBP1 Ribosome binding protein 1 20p12 homolog 180 kDa (dog) 201206_s_at 0.0002058 2.5 RRBP1 ribosome binding protein 1 20p12 homolog 180 kDa (dog) (RRBP1), mRNA. 201250_s_at 0.0001573 3.1 SLC2A1 solute carrier family 2 1p35-p31.3 (facilitated glucose transporter), member 1 (SLC2A1), mRNA. 201261_x_at 0.0003831 4.3 BGN biglycan (BGN), mRNA. Xq28 201302_at 1.57E−05 −3.1 ANXA4 annexin A4 (ANXA4), mRNA. 2p13 201370_s_at 0.0002857 −2.3 CUL3 cullin 3 (CUL3), mRNA. 2q36.3 201376_s_at 0.0001535 −2.4 HNRPF heterogeneous nuclear 10q11.21-q11.22 ribonucleoprotein F (HNRPF), mRNA. 201408_at 3.95E−05 −3.2 PPP1CB protein phosphatase 1, catalytic 2p23 subunit, beta isoform (PPP1CB), transcript variant 2, mRNA. 201425_at 1.80E−06 −2.9 ALDH2 aldehyde dehydrogenase 2 12q24.2 family (mitochondrial) (ALDH2), nuclear gene encoding mitochondrial protein, mRNA. 201427_s_at 0.0004665 −2.5 SEPP1 selenoprotein P, plasma, 1 5q31 (SEPP1), mRNA. 201431_s_at 0.0003957 −4.5 DPYSL3 dihydropyrimidinase-like 3 5q32 (DPYSL3), mRNA. 201432_at 2.09E−05 −3.3 CAT catalase (CAT), mRNA. 11p13 201455_s_at 0.0004393 −2.7 NPEPPS aminopeptidase puromycin 17q21 sensitive (NPEPPS), mRNA. 201482_at 0.0004221 −2.9 QSCN6 quiescin Q6 (QSCN6), transcript 1q24 variant 2, mRNA. 201484_at 0.0001619 −2.2 SUPT4H1 suppressor of Ty 4 homolog 1 17q21-q23 (S. cerevisiae) (SUPT4H1), mRNA. 201487_at 0.0002325 3.1 CTSC cathepsin C (CTSC), transcript 11q14.1-q14.3 variant 1, mRNA. 201496_x_at 0.0005336 −6.1 MYH11 myosin, heavy polypeptide 11, 16p13.13-p13.12 smooth muscle (MYH11), transcript variant SM2, mRNA. 201506_at 0.0003278 3.3 TGFBI transforming growth factor, 5q31 beta-induced, 68 kDa (TGFBI), mRNA. 201529_s_at 0.0001633 −3 RPA1 replication protein A1, 70 kDa 17p13.3 (RPA1), mRNA. 201535_at 6.72E−05 −2.3 UBL3 ubiquitin-like 3 (UBL3), 13q12-q13 mRNA. 201554_x_at 0.0003257 −2.5 GYG glycogenin (GYG), mRNA. 3q24-q25.1 201579_at 0.0007798 2.6 FAT FAT tumor suppressor homolog 4q34-q35 1 (Drosophila) (FAT), mRNA. 201581_at 2.11E−05 −2.4 DJ971N18.2 Hypothetical protein 20p12 DJ971N18.2 201584_s_at 0.0001736 2.3 DDX39 DEAD (Asp-Glu-Ala-Asp) box 19p13.12 polypeptide 39 (DDX39), transcript variant 1, mRNA. 201596_x_at 1.62E−05 4.3 KRT18 keratin 18 (KRT18), transcript 12q13 variant 2, mRNA. 201600_at 3.48E−05 −2.3 PHB2 prohibitin 2 (PHB2), mRNA. 12p13 201666_at 0.0004812 3.4 TIMP1 TIMP metallopeptidase inhibitor Xp11.3-p11.23 1 (TIMP1), mRNA. 201674_s_at 0.0001795 −3 AKAP1 A kinase (PRKA) anchor protein 17q21-q23 1 (AKAP1), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA. 201696_at 0.000121 −2 SFRS4 splicing factor, arginine/serine- 1p35.3 rich 4 (SFRS4), mRNA. 201697_s_at 0.0001256 2.4 DNMT1 DNA (cytosine-5-)- 19p13.2 methyltransferase 1 (DNMT1), mRNA. 201712_s_at 0.0008422 −2.2 RANBP2 RAN binding protein 2 2q12.3 (RANBP2), mRNA. 201737_s_at 5.10E−06 −3.1 6-Mar membrane-associated ring finger 5p15.2 (C3HC4) 6 (MARCH6), mRNA. 201756_at 0.0003533 −2 RPA2 replication protein A2, 32 kDa 1p35 (RPA2), mRNA. 201810_s_at 0.0001904 −3.2 SH3BP5 SH3-domain binding protein 5 3p24.3 (BTK-associated) (SH3BP5), transcript variant 2, mRNA. 201816_s_at 0.0004168 −2.2 GBAS glioblastoma amplified sequence 7p12 (GBAS), mRNA. 201871_s_at 0.0001348 −2 LOC51035 ORF (LOC51035), mRNA. 11q12.3 201891_s_at 0.0007795 2 B2M beta-2-microglobulin (B2M), 15q21-q22.2 mRNA. 201893_x_at 0.0006272 −3.1 DCN decorin (DCN), transcript 12q21.33 variant B, mRNA. 201911_s_at 0.0001467 3.4 FARP1 FERM, RhoGEF (ARHGEF) 13q32.2 and pleckstrin domain protein 1 (chondrocyte-derived) (FARP1), transcript variant 1, mRNA. 201922_at 0.0001538 −2 TINP1 TGF beta-inducible nuclear 5q13.3 protein 1 (TINP1), mRNA. 201960_s_at 0.0002203 −2 MYCBP2 MYC binding protein 2 13q22 (MYCBP2), mRNA. 201973_s_at 0.0004504 2 C7orf28A chromosome 7 open reading 7p22.1 frame 28A (C7orf28A), mRNA. 202016_at 0.0001808 3.2 MEST mesoderm specific transcript 7q32 homolog (mouse) (MEST), transcript variant 3, mRNA. 202028_s_at 0.0002331 3 RPL38 ribosomal protein L38 (RPL38), 17q23-q25 mRNA. 202029_x_at 1.93E−05 −2.1 RPL38 ribosomal protein L38 (RPL38), 17q23-q25 mRNA. 202037_s_at 0.0002558 −3.1 SFRP1 secreted frizzled-related protein 8p12-p11.1 1 (SFRP1), mRNA. 202068_s_at 0.0001171 −4.1 LDLR low density lipoprotein receptor 19p13.3 (familial hypercholesterolemia) (LDLR), mRNA. 202073_at 4.49E−05 −2.6 OPTN optineurin (OPTN), transcript 10p13 variant 2, mRNA. 202105_at 3.00E−07 −3.2 IGBP1 immunoglobulin (CD79A) Xq13.1-q13.3 binding protein 1 (IGBP1), mRNA. 202119_s_at 0.0002779 −3.2 CPNE3 copine III (CPNE3), mRNA. 8q21.3 202139_at 0.0004872 −2.1 AKR7A2 aldo-keto reductase family 7, 1p35.1-p36.23 member A2 (aflatoxin aldehyde reductase) (AKR7A2), mRNA. 202148_s_at 0.0006205 2.2 PYCR1 pyrroline-5-carboxylate 17q25.3 reductase 1 (PYCR1), transcript variant 2, mRNA. 202156_s_at 0.0004765 −2.8 CUGBP2 CUG triplet repeat, RNA 10p13 binding protein 2 (CUGBP2), transcript variant 2, mRNA. 202157_s_at 9.00E−07 −6.1 CUGBP2 CUG triplet repeat, RNA 10p13 binding protein 2 (CUGBP2), transcript variant 2, mRNA. 202158_s_at 2.99E−05 −4.2 CUGBP2 CUG triplet repeat, RNA 10p13 binding protein 2 (CUGBP2), transcript variant 2, mRNA. 202172_at 0.0006154 −2.4 ZNF161 zinc finger protein 161 17q23.2 (ZNF161), mRNA. 202202_s_at 0.0002996 3.4 LAMA4 laminin, alpha 4 (LAMA4), 6q21 mRNA. 202214_s_at 0.0005849 −2 CUL4B Cullin 4B Xq23 202232_s_at 0.0002955 −2.2 hfl-B5 dendritic cell protein (hfl-B5), 11p13 mRNA. 202259_s_at 3.74E−05 −3.2 PFAAP5 phosphonoformate immuno- 13q12-q13 associated protein 5 (PFAAP5), mRNA. 202260_s_at 0.0005909 −2.2 STXBP1 syntaxin binding protein 1 9q34.1 (STXBP1), transcript variant 2, mRNA. 202286_s_at 0.0003361 5.5 TACSTD2 tumor-associated calcium signal 1p32-p31 transducer 2 (TACSTD2), mRNA. 202292_x_at 0.0001802 2.4 LYPLA2 lysophospholipase II (LYPLA2), 1p36.12-p35.1 mRNA. 202297_s_at 6.25E−05 2.2 RER1 RER1 retention in endoplasmic 1pter-q24 reticulum 1 homolog (S. cerevisiae) (RER1), mRNA. 202314_at 0.0001115 −2.6 CYP51A1 cytochrome P450, family 51, 7q21.2-q21.3 subfamily A, polypeptide 1 (CYP51A1), mRNA. 202350_s_at 0.0002121 −3.7 MATN2 matrilin 2 (MATN2), transcript 8q22 variant 2, mRNA. 202364_at 0.0002246 −2.5 MXI1 MAX interactor 1 (MXI1), 10q24-q25 transcript variant 3, mRNA. 202378_s_at 6.45E−05 −2.2 LEPROT leptin receptor overlapping 1p31.2 transcript (LEPROT), mRNA. 202404_s_at 0.000452 2.9 COL1A2 collagen, type I, alpha 2 7q22.1 (COL1A2), mRNA. 202429_s_at 0.0001255 −2.4 PPP3CA protein phosphatase 3 (formerly 4q21-q24 2B), catalytic subunit, alpha isoform (calcineurin A alpha) (PPP3CA), mRNA. 202464_s_at 0.0009823 3.5 PFKFB3 6-phosphofructo-2- 10p14-p15 kinase/fructose-2,6- biphosphatase 3 202465_at 9.80E−06 4.8 PCOLCE procollagen C-endopeptidase 7q22 enhancer (PCOLCE), mRNA. 202468_s_at 7.84E−05 −2.5 CTNNAL1 catenin (cadherin-associated 9q31.2 protein), alpha-like 1 (CTNNAL1), mRNA. 202502_at 5.08E−05 −2 ACADM acyl-Coenzyme A 1p31 dehydrogenase, C-4 to C-12 straight chain (ACADM), nuclear gene encoding mitochondrial protein, mRNA. 202510_s_at 1.14E−05 3.7 TNFAIP2 tumor necrosis factor, alpha- 14q32 induced protein 2 (TNFAIP2), mRNA. 202512_s_at 6.24E−05 −2.2 APG5L APG5 autophagy 5-like (S. cerevisiae) 6q21 (APG5L), mRNA. 202536_at 0.0002234 −2 CHMP2B chromatin modifying protein 2B 3p12.1 (CHMP2B), mRNA. 202546_at 0.0004572 5.6 VAMP8 vesicle-associated membrane 2p12-p11.2 protein 8 (endobrevin) (VAMP8), mRNA. 202547_s_at 6.98E−05 3 ARHGEF7 Rho guanine nucleotide 13q34 exchange factor (GEF) 7 (ARHGEF7), transcript variant 1, mRNA. 202573_at 0.0002474 2 CSNK1G2 casein kinase 1, gamma 2 19p13.3 (CSNK1G2), mRNA. 202581_at 0.0002675 2.8 HSPA1B heat shock 70 kDa protein 1B 6p21.3 (HSPA1B), mRNA. 202630_at 6.64E−05 −2.7 APPBP2 amyloid beta precursor protein 17q21-q23 (cytoplasmic tail) binding protein 2 (APPBP2), mRNA. 202665_s_at 0.0003645 2.9 WASPIP Wiskott-Aldrich syndrome 2q31.1 protein interacting protein (WASPIP), mRNA. 202722_s_at 0.0002949 2.1 GFPT1 glutamine-fructose-6-phosphate 2p13 transaminase 1 (GEPT1), mRNA. 202723_s_at 2.20E−06 −4 FOXO1A forkhead box O1A 13q14.1 (rhabdomyosarcoma) (FOXO1A), mRNA. 202724_s_at 6.00E−07 −3.3 FOXO1A forkhead box O1A 13q14.1 (rhabdomyosarcoma) (FOXO1A), mRNA. 202731_at 0.0008149 −2.6 PDCD4 programmed cell death 4 10q24 (neoplastic transformation inhibitor) (PDCD4), transcript variant 1, mRNA. 202733_at 0.0005751 3 P4HA2 procollagen-proline, 2- 5q31 oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II (P4HA2), transcript variant 3, mRNA. 202746_at 0.0005864 −6.4 ITM2A integral membrane protein 2A Xq13.3-Xq21.2 (ITM2A), mRNA. 202749_at 0.0009431 −2.2 WRB Tryptophan rich basic protein 21q22.3 202761_s_at 0.0003908 −2.3 SYNE2 spectrin repeat containing, 14q23.2 nuclear envelope 2 (SYNE2), transcript variant 4, mRNA. 202780_at 0.0009309 −2 OXCT1 3-oxoacid CoA transferase 1 5p13.1 (OXCT1), nuclear gene encoding mitochondrial protein, mRNA. 202820_at 1.90E−05 3.3 AHR aryl hydrocarbon receptor 7p15 (AHR), mRNA. 202825_at 0.0004002 −2.1 SLC25A4 solute carrier family 25 4q35 (mitochondrial carrier; adenine nucleotide translocator), member 4 (SLC25A4), nuclear gene encoding mitochondrial protein, mRNA. 202888_s_at 0.0005702 4.7 ANPEP alanyl (membrane) 15q25-q26 aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150) (ANPEP), mRNA. 202899_s_at 5.55E−05 −2.8 SFRS3 splicing factor, arginine/serine- 6p21 rich 3 (SFRS3), mRNA. 202908_at 5.90E−06 −3.4 WFS1 Wolfram syndrome 1 4p16 (wolframin) (WFS1), mRNA. 202911_at 0.0008837 −2.1 MSH6 mutS homolog 6 (E. coli) 2p16 (MSH6), mRNA. 202920_at 4.60E−06 −4.2 ANK2 ankyrin 2, neuronal (ANK2), 4q25-q27 transcript variant 2, mRNA. 202952_s_at 2.37E−05 7.6 ADAM12 ADAM metallopeptidase 10q26.3 domain 12 (meltrin alpha) (ADAM12), transcript variant 1, mRNA. 202954_at 0.0006434 2.8 UBE2C ubiquitin-conjugating enzyme 20q13.12 E2C (UBE2C), transcript variant 1, mRNA. 202957_at 0.000374 2.7 HCLS1 hematopoietic cell-specific Lyn 3q13 substrate 1 (HCLS1), mRNA. 202968_s_at 0.0001551 2.3 DYRK2 dual-specificity tyrosine-(Y)- 12q15 phosphorylation regulated kinase 2 (DYRK2), transcript variant 1, mRNA. 202975_s_at 2.87E−05 −3.6 RHOBTB3 Rho-related BTB domain 5q15 containing 3 (RHOBTB3), mRNA. 202992_at 0.000519 −5.4 C7 complement component 7 (C7), 5p13 mRNA. 202998_s_at 0.0006468 3 LOXL2 lysyl oxidase-like 2 (LOXL2), 8p21.3-p21.2 mRNA. 203088_at 0.0008436 −4.5 FBLN5 fibulin 5 (FBLN5), mRNA. 14q32.1 203156_at 3.37E−05 −2.4 AKAP11 A kinase (PRKA) anchor protein 13q14.11 11 (AKAP11), transcript variant 1, mRNA. 203166_at 0.0001939 −2.3 CFDP1 craniofacial development protein 16q22.2-q22.3 1 (CFDP1), mRNA. 203178_at 0.0002428 −3.3 GATM glycine amidinotransferase (L- 15q21.1 arginine:glycine amidinotransferase) (GATM), mRNA. 203249_at 0.0004075 −2.5 EZH1 enhancer of zeste homolog 1 17q21.1-q21.3 (Drosophila) (EZH1), mRNA. 203297_s_at 4.33E−05 2.4 JARID2 Jumonji, AT rich interactive 6p24-p23 domain 2 (JARID2), mRNA. 203298_s_at 0.0005468 2.1 JARID2 Jumonji, AT rich interactive 6p24-p23 domain 2 (JARID2), mRNA. 203349_s_at 7.26E−05 2.8 ETV5 ets variant gene 5 (ets-related 3q28 molecule) (ETV5), mRNA. 203356_at 7.77E−05 −2.6 CAPN7 calpain 7 (CAPN7), mRNA. 3p24 203358_s_at 2.44E−05 2.9 EZH2 enhancer of zeste homolog 2 7q35-q36 (Drosophila) (EZH2), transcript variant 2, mRNA. 203401_at 0.0003991 −3.8 PRPS2 phosphoribosyl pyrophosphate Xp22.3-p22.2 synthetase 2 (PRPS2), mRNA. 203423_at 0.0008061 −3.9 RBP1 retinol binding protein 1, 3q23 cellular (RBP1), mRNA. 203424_s_at 0.0007037 −3.8 IGFBP5 insulin-like growth factor 2q33-q36 binding protein 5 (IGFBP5), mRNA. 203427_at 7.05E−05 −2.6 ASF1A ASF1 anti-silencing function 1 6q22.31 homolog A (S. cerevisiae) (ASF1A), mRNA. 203450_at 0.0007322 −2.1 PGEA1 PKD2 interactor, golgi and 22q12 endoplasmic reticulum associated 1 (PGEA1), transcript variant 1, mRNA. 203455_s_at 0.0005583 2 SAT spermidine/spermine N1- Xp22.1 acetyltransferase (SAT), mRNA. 203459_s_at 8.97E−05 2.1 VPS16 vacuolar protein sorting 16 20p13-p12 (yeast) (VPS16), transcript variant 2, mRNA. 203468_at 0.0009911 2.3 CDK10 cyclin-dependent kinase (CDC2- 16q24 like) 10 (CDK10), transcript variant 2, mRNA. 203476_at 1.65E−05 2.6 TPBG trophoblast glycoprotein 6q14-q15 (TPBG), mRNA. 203493_s_at 0.0009017 −2.1 PIG8 translokin (PIG8), mRNA. 11q21 203494_s_at 0.0001224 −2.2 PIG8 translokin (PIG8), mRNA. 11q21 203505_at 0.0001234 2.7 ABCA1 ATP-binding cassette, sub- 9q31.1 family A (ABC1), member 1 203549_s_at 0.0001406 3.9 LPL lipoprotein lipase (LPL), 8p22 mRNA. 203599_s_at 0.0004137 −2 WBP4 WW domain binding protein 4 13q14.11 (formin binding protein 21) (WBP4), mRNA. 203640_at 0.0002347 −2 MBNL2 muscleblind-like 2 (Drosophila) 13q32.1 (MBNL2), transcript variant 3, mRNA. 203657_s_at 0.0007798 −2.3 CTSF cathepsin F (CTSF), mRNA. 11q13 203680_at 9.00E−07 −6.1 PRKAR2B protein kinase, cAMP- 7q22 dependent, regulatory, type II, beta (PRKAR2B), mRNA. 203692_s_at 0.0005974 2.2 E2F3 E2F transcription factor 3 6p22 (E2F3), mRNA. 203695_s_at 0.0009082 −2.2 DFNA5 deafness, autosomal dominant 5 7p15 (DFNA5), mRNA. 203758_at 0.0002672 −2 CTSO cathepsin O (CTSO), mRNA. 4q31-q32 203762_s_at 0.0003113 −2.1 D2LIC dynein 2 light intermediate chain 2p25.1-p24.1 (D2LIC), transcript variant 1, mRNA. 203799_at 1.06E−05 −3.3 CD302 CD302 antigen (CD302), 2q24.2 mRNA. 203803_at 3.79E−05 −3.9 PCYOX1 prenylcysteine oxidase 1 2p13.3 (PCYOX1), mRNA. 203845_at 0.0001562 −2.8 PCAF p300/CBP-associated factor 3p24 (PCAF), mRNA. 203878_s_at 2.11E−05 3.7 MMP11 matrix metallopeptidase 11 22q11.23 (stromelysin 3) (MMP11), mRNA. 203888_at 0.0008536 −4 THBD thrombomodulin (THBD), 20p12-cen mRNA. 203897_at 7.35E−05 −2.2 LOC57149 hypothetical protein A-211C6.1 16p11.2 (LOC57149), mRNA. 203908_at 0.0008304 2.7 SLC4A4 solute carrier family 4, sodium 4q21 bicarbonate cotransporter, member 4 (SLC4A4), mRNA. 203936_s_at 0.0002019 9.4 MMP9 matrix metallopeptidase 9 20q11.2-q13.1 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase) (MMP9), mRNA. 204004_at 1.50E−06 −3.2 PAWR PRKC, apoptosis, WT1, 12q21 regulator 204029_at 0.0005472 2.4 CELSR2 cadherin, EGF LAG seven-pass 1p21 G-type receptor 2 (flamingo homolog, Drosophila) (CELSR2), mRNA. 204041_at 0.0003564 −6.4 MAOB Monoamine oxidase B Xp11.23 204045_at 2.00E−07 −4.5 TCEAL1 Transcription elongation factor Xq22.1 A (SII)-like 1 204078_at 0.0001645 2.6 SC65 synaptonemal complex protein 17q21.2 SC65 (SC65), mRNA. 204082_at 0.0002318 −2.8 PBX3 pre-B-cell leukemia 9q33-q34 transcription factor 3 (PBX3), mRNA. 204109_s_at 0.0006487 2.5 NFYA nuclear transcription factor Y, 6p21.3 alpha (NFYA), transcript variant 2, mRNA. 204136_at 7.18E−05 3.4 COL7A1 collagen, type VII, alpha 1 3p21.1 (epidermolysis bullosa, dystrophic, dominant and recessive) (COL7A1), mRNA. 204184_s_at 9.26E−05 3 ADRBK2 adrenergic, beta, receptor kinase 22q12.1 2 (ADRBK2), mRNA. 204235_s_at 2.45E−05 −4.3 GULP1 GULP, engulfment adaptor PTB 2q32.3-q33 domain containing 1 (GULP1), mRNA. 204237_at 1.32E−05 −3.2 GULP1 GULP, engulfment adaptor PTB 2q32.3-q33 domain containing 1 (GULP1), mRNA. 204256_at 0.0008289 2.1 ELOVL6 ELOVL family member 6, 4q25 elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3- like, yeast) (ELOVL6), mRNA. 204285_s_at 1.20E−06 7.7 PMAIP1 phorbol-12-myristate-13- 18q21.32 acetate-induced protein 1 (PMAIP1), mRNA. 204286_s_at 3.50E−06 8.5 PMAIP1 phorbol-12-myristate-13- 18q21.32 acetate-induced protein 1 (PMAIP1), mRNA. 204387_x_at 7.88E−05 2.6 MRP63 mitochondrial ribosomal protein 13p11.1-q11 63 (MRP63), nuclear gene encoding mitochondrial protein, mRNA. 204454_at 0.0002053 −2.6 LDOC1 leucine zipper, down-regulated Xq27 in cancer 1 (LDOC1), mRNA. 204473_s_at 0.0009569 2 ZNF592 zinc finger protein 592 15q25.3 (ZNF592), mRNA. 204493_at 0.0003505 2.7 BID BH3 interacting domain death 22q11.1 agonist (BID), transcript variant 3, mRNA. 204495_s_at 0.0006319 2.8 DKFZP434H132 DKFZP434H132 protein 15q23 204531_s_at 0.0004972 2.5 BRCA1 breast cancer 1, early onset 17q21 (BRCA1), transcript variant BRCA1-delta9-11, mRNA. 204595_s_at 1.40E−06 10.5 STC1 stanniocalcin 1 (STC1), mRNA. 8p21-p11.2 204597_x_at 0.0001207 7.5 STC1 stanniocalcin 1 (STC1), mRNA. 8p21-p11.2 204619_s_at 0.0005599 4.6 CSPG2 Chondroitin sulfate 5q14.3 proteoglycan 2 (versican) 204639_at 1.47E−05 4.2 ADA adenosine deaminase (ADA), 20q12-q13.11 mRNA. 204641_at 0.0006499 4.6 NEK2 NIMA (never in mitosis gene a)- 1q32.2-q41 related kinase 2 (NEK2), mRNA. 204669_s_at 0.0008759 2 RNF24 ring finger protein 24 (RNF24), 20p13-p12.1 mRNA. 204731_at 0.0002926 −3.2 TGFBR3 transforming growth factor, beta 1p33-p32 receptor III (betaglycan, 300 kDa) (TGFBR3), mRNA. 204735_at 3.38E−05 3.5 PDE4A phosphodiesterase 4A, cAMP- 19p13.2 specific (phosphodiesterase E2 dunce homolog, Drosophila) (PDE4A), mRNA. 204749_at 0.0005462 −3 NAP1L3 nucleosome assembly protein 1- Xq21.3-q22 like 3 (NAP1L3), mRNA. 204786_s_at 1.59E−05 2.8 IFNAR2 interferon (alpha, beta and 21q22.11 omega) receptor 2 (IFNAR2), transcript variant 1, mRNA. 204793_at 1.31E−05 −4.2 GPRASP1 G protein-coupled receptor Xq22.1 associated sorting protein 1 (GPRASP1), mRNA. 204939_s_at 0.0007407 −5.7 PLN phospholamban (PLN), mRNA. 6q22.1 204994_at 4.91E−05 4.5 MX2 myxovirus (influenza virus) 21q22.3 resistance 2 (mouse) (MX2), mRNA. 205068_s_at 2.40E−06 3.8 ARHGAP26 Rho GTPase activating protein 5q31 26 (ARHGAP26), mRNA. 205079_s_at 0.0003985 −2 MPDZ multiple PDZ domain protein 9p24-p22 (MPDZ), mRNA. 205226_at 0.0004657 −3 PDGFRL platelet-derived growth factor 8p22-p21.3 receptor-like (PDGFRL), mRNA. 205231_s_at 0.0008847 −2 EPM2A epilepsy, progressive myoclonus 6q24 type 2A, Lafora disease (laforin) (EPM2A), transcript variant 1, mRNA. 205241_at 4.20E−05 4.5 SCO2 SCO cytochrome oxidase 22q13.33 deficient homolog 2 (yeast) (SCO2), nuclear gene encoding mitochondrial protein, mRNA. 205259_at 0.0002039 −2.5 NR3C2 nuclear receptor subfamily 3, 4q31.1 group C, member 2 (NR3C2), mRNA. 205269_at 4.00E−06 8.7 LCP2 lymphocyte cytosolic protein 2 5q33.1-qter (SH2 domain containing leukocyte protein of 76 kDa) (LCP2), mRNA. 205270_s_at 0.0006743 6.7 LCP2 lymphocyte cytosolic protein 2 5q33.1-qter (SH2 domain containing leukocyte protein of 76 kDa) (LCP2), mRNA. 205304_s_at 0.0007499 2.4 KCNJ8 potassium inwardly-rectifying 12p11.23 channel, subfamily J, member 8 (KCNJ8), mRNA. 205353_s_at 3.92E−05 −3.3 PBP prostatic binding protein (PBP), 12q24.23 mRNA. 205367_at 0.0001487 2.7 APS adaptor protein with pleckstrin 7q22 homology and src homology 2 domains (APS), mRNA. 205370_x_at 0.0004381 2.9 DBT dihydrolipoamide branched 1p31 chain transacylase E2 (DBT), mRNA. 205381_at 0.0001503 −5.4 LRRC17 leucine rich repeat containing 17 7q22.1 (LRRC17), transcript variant 1, mRNA. 205406_s_at 3.91E−05 2.5 SPA17 sperm autoantigenic protein 17 11q24.2 (SPA17), mRNA. 205412_at 6.30E−06 −2.7 ACAT1 acetyl-Coenzyme A 11q22.3-q23.1 acetyltransferase 1 (acetoacetyl Coenzyme A thiolase) (ACAT1), nuclear gene encoding mitochondrial protein, mRNA. 205463_s_at 0.000255 3.1 PDGFA Platelet-derived growth factor 7p22 alpha polypeptide 205466_s_at 6.17E−05 −4.7 HS3ST1 heparan sulfate (glucosamine) 3- 4p16 O-sulfotransferase 1 (HS3ST1), mRNA. 205479_s_at 0.000306 3.8 PLAU plasminogen activator, 10q24 urokinase (PLAU), mRNA. 205483_s_at 0.0001248 6.9 G1P2 interferon, alpha-inducible 1p36.33 protein (clone IFI-15K) (G1P2), mRNA. 205532_s_at 0.0004946 2.8 CDH6 cadherin 6, type 2, K-cadherin 5p15.1-p14 (fetal kidney) (CDH6), mRNA. 205572_at 0.0003915 5.4 ANGPT2 angiopoietin 2 (ANGPT2), 8p23.1 mRNA. 205687_at 0.000463 2 UBPH similar to ubiquitin binding 16p12 protein (UBPH), mRNA. 205771_s_at 0.0009058 −2.3 AKAP7 A kinase (PRKA) anchor protein 6q23 7 (AKAP7), transcript variant alpha, mRNA. 205812_s_at 9.00E−06 2.4 TMED9 transmembrane emp24 protein 5q35.3 transport domain containing 9 (TMED9), mRNA. 205849_s_at 0.0005492 −2 UQCRB ubiquinol-cytochrome c 8q22 reductase binding protein (UQCRB), mRNA. 205862_at 7.65E−05 −8.6 GREB1 GREB1 protein (GREB1), 2p25.1 transcript variant a, mRNA. 205871_at 0.0003369 3.1 PLGLB1 plasminogen-like B1 (PLGLB1), 2 mRNA. 205943_at 0.0004032 4.4 TDO2 tryptophan 2,3-dioxygenase 4q31-q32 (TDO2), mRNA. 205961_s_at 0.0002574 −2.9 PSIP1 PC4 and SFRS1 interacting 9p22.3 protein 1 (PSIP1), transcript variant 2, mRNA. 206026_s_at p < 1e−07 29.1 TNFAIP6 tumor necrosis factor, alpha- 2q23.3 induced protein 6 (TNFAIP6), mRNA. 206158_s_at 0.0006831 −2.2 ZNF9 zinc finger protein 9 (a cellular 3q21 retroviral nucleic acid binding protein) (ZNF9), mRNA. 206169_x_at 0.0008428 3.9 RoXaN Zinc finger CCCH-type 22q13.2 containing 7B 206211_at 0.0002057 −8.9 SELE selectin E (endothelial adhesion 1q22-q25 molecule 1) (SELE), mRNA. 206247_at 9.38E−05 3.3 MICB MHC class I polypeptide-related 6p21.3 sequence B (MICB), mRNA. 206359_at 0.0004232 −3.5 SOCS3 Suppressor of cytokine signaling 3 17q25.3 206377_at 2.40E−06 6 FOXF2 forkhead box F2 (FOXF2), 6p25.3 mRNA. 206435_at 0.0009321 3.2 GALGT UDP-N-acetyl-alpha-D- 12q13.3 galactosamine:(N- acetylneuraminyl)- galactosylglucosylceramide N- acetylgalactosaminyltransferase (GalNAc-T) (GALGT), mRNA. 206483_at 0.0009412 2 LRRC6 leucine rich repeat containing 6 8q24.22 (LRRC6), mRNA. 206551_x_at 0.0001129 2.7 DRE1 DRE1 protein 3q27.1 206571_s_at 0.000131 2.7 MAP4K4 mitogen-activated protein kinase 2q11.2-q12 kinase kinase kinase 4 (MAP4K4), transcript variant 1, mRNA. 206621_s_at 0.0002653 −2.3 WBSCR1 Williams-Beuren syndrome 7q11.23 chromosome region 1 (WBSCR1), transcript variant 2, mRNA. 206637_at 3.52E−05 4.8 P2RY14 purinergic receptor P2Y, G- 3q21-q25 protein coupled, 14 (P2RY14), mRNA. 206792_x_at 6.82E−05 3.7 PDE4C phosphodiesterase 4C, cAMP- 19p13.11 specific (phosphodiesterase E1 dunce homolog, Drosophila) (PDE4C), mRNA. 206809_s_at 0.0004239 −2.8 HNRPA3P1 Heterogeneous nuclear 10q11.21 ribonucleoprotein A3 pseudogene 1 206857_s_at 0.0002413 2.5 FKBP1B FK506 binding protein 1B, 12.6 kDa 2p23.3 (FKBP1B), transcript variant 1, mRNA. 206874_s_at 9.71E−05 −2.9 SLK STE20-like kinase (yeast) 10q25.1 206927_s_at 0.0004319 3.3 GUCY1A2 guanylate cyclase 1, soluble, 11q21-q22 alpha 2 (GUCY1A2), mRNA. 207040_s_at 1.56E−05 −2.6 ST13 suppression of tumorigenicity 13 22q13.2 (colon carcinoma) (Hsp70 interacting protein) (ST13), mRNA. 207132_x_at 0.0002292 −2.5 PFDN5 prefoldin 5 (PFDN5), transcript 12q12 variant 1, mRNA. 207147_at 0.0007438 3.3 DLX2 distal-less homeo box 2 (DLX2), 2q32 mRNA. 207170_s_at 1.76E−05 −2.6 LETMD1 LETM1 domain containing 1 12q13.12 (LETMD1), transcript variant 3, mRNA. 207239_s_at 0.0002121 2.2 PCTK1 PCTAIRE protein kinase 1 Xp11.3-p11.23 (PCTK1), transcript variant 1, mRNA. 207365_x_at 6.06E−05 3.7 USP34 Ubiquitin specific protease 34 2p15 207386_at 0.0009685 2.7 CYP7B1 cytochrome P450, family 7, 8q21.3 subfamily B, polypeptide 1 (CYP7B1), mRNA. 207598_x_at 0.0001463 3.5 XRCC2 X-ray repair complementing 7q36.1 defective repair in Chinese hamster cells 2 (XRCC2), mRNA. 207688_s_at 0.0006478 2.4 LOC387933 PREDICTED: similar to 13 heterogeneous nuclear ribonucleoprotein A3 (LOC387933), mRNA. 207730_x_at 0.0002746 3.1 FLJ20700 hypothetical protein FLJ20700 19p13.3 207761_s_at 1.38E−05 −4.2 DKFZP586A0522 DKFZP586A0522 protein 12q13.12 (DKFZP586A0522), mRNA. 207961_x_at 0.0006679 −3.8 MYH11 myosin, heavy polypeptide 11, 16p13.13-p13.12 smooth muscle (MYH11), transcript variant SM1, mRNA. 207974_s_at 0.0001511 −2.1 SKP1A S-phase kinase-associated 5q31 protein 1A (p19A) (SKP1A), transcript variant 2, mRNA. 207983_s_at 0.0009431 −2.3 STAG2 stromal antigen 2 (STAG2), Xq25 mRNA. 208092_s_at 0.0004178 2.9 FAM49A family with sequence similarity 2p24.3-p24.2 49, member A (FAM49A), mRNA. 208137_x_at 0.0008157 2.6 ZNF611 Zinc finger protein 611 19q13.41 208238_x_at 0.0007093 2.4 LZLP leucine zipper-like protein 11q13.1 208246_x_at 8.09E−05 3.6 FLJ20006 hypothetical protein FLJ20006 16q23.1 208248_x_at 5.35E−05 −3.5 APLP2 amyloid beta (A4) precursor-like 11q24 protein 2 (APLP2), mRNA. 208540_x_at 0.0007507 2 S100A14 S100 calcium binding protein 7q22-q31.1 A14 (calgizzarin) 208626_s_at 0.000509 −2.1 VAT1 vesicle amine transport protein 1 17q21 homolog (T californica) (VAT1), mRNA. 208631_s_at 0.0003804 −2.3 HADHA hydroxyacyl-Coenzyme A 2p23 dehydrogenase/3-ketoacyl- Coenzyme A thiolase/enoyl- Coenzyme A hydratase (trifunctional protein), alpha subunit (HADHA), mRNA. 208635_x_at 8.57E−05 −2 NACA nascent-polypeptide-associated 12q23-q24.1 complex alpha polypeptide (NACA), mRNA. 208643_s_at 2.41E−05 −2.9 XRCC5 X-ray repair complementing 2q35 defective repair in Chinese hamster cells 5 (double-strand- break rejoining; Ku autoantigen, 80 kDa) (XRCC5), mRNA. 208647_at 0.0004172 −2.1 FDFT1 farnesyl-diphosphate 8p23.1-p22 farnesyltransferase 1 (FDFT1), mRNA. 208653_s_at 0.0002993 3 CD164 CD164 antigen, sialomucin 6q21 (CD164), mRNA. 208655_at 0.0001893 −2.8 CCNI Cyclin I 4q21.1 208658_at 0.0005959 2 PDIA4 protein disulfide isomerase 7q35 family A, member 4 (PDIA4), mRNA. 208662_s_at 0.0009682 −2.1 TTC3 tetratricopeptide repeat domain 21q22.2 3 (TTC3), transcript variant 2, mRNA. 208666_s_at 5.00E−07 −4.5 ST13 suppression of tumorigenicity 13 22q13.2 (colon carcinoma) (Hsp70 interacting protein) (ST13), mRNA. 208667_s_at 4.53E−05 −2.8 ST13 suppression of tumorigenicity 13 22q13.2 (colon carcinoma) (Hsp70 interacting protein) (ST13), mRNA. 208671_at 0.0005205 −2 TDE2 tumor differentially expressed 2 6q22.31 (TDE2), mRNA. 208673_s_at 0.0005001 −2.2 SFRS3 splicing factor, arginine/serine- 6p21 rich 3 (SFRS3), mRNA. 208697_s_at 4.85E−05 −2.4 EIF3S6 eukaryotic translation initiation 8q22-q23 factor 3, subunit 6 48 kDa (EIF3S6), mRNA. 208703_s_at 0.0002231 −3.7 APLP2 amyloid beta (A4) precursor-like 11q24 protein 2 (APLP2), mRNA. 208704_x_at 4.90E−05 −3.6 APLP2 amyloid beta (A4) precursor-like 11q24 protein 2 (APLP2), mRNA. 208740_at 7.40E−05 −2.2 SAP18 sin3-associated polypeptide, 13q12.11 18 kDa (SAP18), mRNA. 208760_at 7.17E−05 −2.7 UBE2I Ubiquitin-conjugating enzyme 16p13.3 E2I (UBC9 homolog, yeast) 208770_s_at 0.0005681 −2 EIF4EBP2 eukaryotic translation initiation 10q21-q22 factor 4E binding protein 2 (EIF4EBP2), mRNA. 208771_s_at 2.10E−05 −2.6 LTA4H leukotriene A4 hydrolase 12q22 (LTA4H), mRNA. 208781_x_at 0.0006007 −2.2 SNX3 sorting nexin 3 (SNX3), 6q21 transcript variant 1, mRNA. 208791_at 0.0001028 −4.4 CLU clusterin (complement lysis 8p21-p12 inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone- repressed prostate message 2, apolipoprotein J) (CLU), transcript variant 1, mRNA. 208792_s_at 0.0001175 −4.5 CLU clusterin (complement lysis 8p21-p12 inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone- repressed prostate message 2, apolipoprotein J) (CLU), transcript variant 1, mRNA. 208794_s_at 1.47E−05 2.4 SMARCA4 SWI/SNF related, matrix 19p13.2 associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4), mRNA. 208796_s_at 0.0001639 −2.6 CCNG1 cyclin G1 (CCNG1), transcript 5q32-q34 variant 2, mRNA. 208848_at 1.50E−06 −3.7 ADH5 alcohol dehydrogenase 5 (class 4q21-q25 III), chi polypeptide (ADH5), mRNA. 208860_s_at 0.0001719 −2 ATRX alpha thalassemia/mental Xq13.1-q21.1 retardation syndrome X-linked (RAD54 homolog, S. cerevisiae) (ATRX), transcript variant 2, mRNA. 208873_s_at 5.10E−05 −2.1 C5orf18 chromosome 5 open reading 5q22-q23 frame 18 (C5orf18), mRNA. 208920_at 0.0003111 −2.3 SRI sorcin (SRI), transcript variant 2, 7q21.1 mRNA. 208925_at 0.0005429 −2.3 C3orf4 chromosome 3 open reading 3p11-q11 frame 4 (C3orf4), mRNA. 208950_s_at 0.0004293 −2.3 ALDH7A1 aldehyde dehydrogenase 7 5q31 family, member A1 (ALDH7A1), mRNA. 208951_at 4.20E−05 −2.8 ALDH7A1 aldehyde dehydrogenase 7 5q31 family, member A1 (ALDH7A1), mRNA. 208962_s_at 0.0003548 −2.4 FADS1 fatty acid desaturase 1 (FADS1), 11q12.2-q13.1 mRNA. 208990_s_at 5.40E−05 −2.2 HNRPH3 heterogeneous nuclear 10q22 ribonucleoprotein H3 (2H9) (HNRPH3), transcript variant 2H9A, mRNA. 209009_at 1.50E−06 −3 ESD esterase D/formylglutathione 13q14.1-q14.2 hydrolase (ESD), mRNA. 209030_s_at 3.07E−05 2.6 IGSF4 immunoglobulin superfamily, 11q23.2 member 4 (IGSF4), mRNA. 209034_at 3.20E−06 −4.5 PNRC1 proline-rich nuclear receptor 6q15 coactivator 1 (PNRC1), mRNA. 209068_at 1.00E−06 −3.5 HNRPDL heterogeneous nuclear 4q13-q21 ribonucleoprotein D-like (HNRPDL), transcript variant 2, mRNA. 209081_s_at 8.30E−06 5 COL18A1 collagen, type XVIII, alpha 1 21q22.3 (COL18A1), transcript variant 2, mRNA. 209082_s_at 4.04E−05 5.1 COL18A1 collagen, type XVIII, alpha 1 21q22.3 (COL18A1), transcript variant 2, mRNA. 209137_s_at 0.0007917 −2.1 USP10 ubiquitin specific peptidase 10 16q24.1 (USP10), mRNA. 209143_s_at 0.0009179 −2.1 CLNS1A chloride channel, nucleotide- 11q13.5-q14 sensitive, 1A (CLNS1A), mRNA. 209146_at 0.0002317 −3.2 SC4MOL sterol-C4-methyl oxidase-like 4q32-q34 (SC4MOL), transcript variant 2, mRNA. 209169_at 0.0003677 4.2 GPM6B glycoprotein M6B (GPM6B), Xp22.2 transcript variant 1, mRNA. 209170_s_at 0.00014 5.8 GPM6B glycoprotein M6B (GPM6B), Xp22.2 transcript variant 4, mRNA. 209243_s_at 3.90E−06 −7.7 PEG3 paternally expressed 3 (PEG3), 19q13.4 mRNA. 209305_s_at 0.0001816 −3.7 GADD45B growth arrest and DNA-damage- 19p13.3 inducible, beta (GADD45B), mRNA. 209337_at 4.01E−05 −3 PSIP1 PC4 and SFRS1 interacting 9p22.3 protein 1 (PSIP1), transcript variant 2, mRNA. 209357_at 5.76E−05 −3.3 CITED2 Cbp/p300-interacting 6q23.3 transactivator, with Glu/Asp- rich carboxy-terminal domain, 2 (CITED2), mRNA. 209360_s_at 7.44E−05 4.8 RUNX1 runt-related transcription factor 21q22.3 1 (acute myeloid leukemia 1; aml1 oncogene) (RUNX1), transcript variant 1, mRNA. 209384_at 0.0002565 −2 PROSC proline synthetase co-transcribed 8p11.2 homolog (bacterial) (PROSC), mRNA. 209385_s_at 3.63E−05 −2.6 PROSC proline synthetase co-transcribed 8p11.2 homolog (bacterial) (PROSC), mRNA. 209447_at 3.84E−05 −2.5 SYNE1 spectrin repeat containing, 6q25 nuclear envelope 1 (SYNE1), transcript variant alpha, mRNA. 209512_at 3.90E−06 −3.9 HSDL2 hydroxysteroid dehydrogenase 9q32 like 2 (HSDL2), mRNA. 209513_s_at 1.94E−05 −3.9 HSDL2 hydroxysteroid dehydrogenase 9q32 like 2 (HSDL2), mRNA. 209596_at 4.80E−06 6.9 MXRA5 matrix-remodelling associated 5 Xp22.33 (MXRA5), mRNA. 209605_at 0.0004157 −2.4 TST thiosulfate sulfurtransferase 22q13.1 (rhodanese) (TST), nuclear gene encoding mitochondrial protein, mRNA. 209612_s_at 0.0001328 −4.5 ADH1B alcohol dehydrogenase IB (class 4q21-q23 I), beta polypeptide (ADH1B), mRNA. 209613_s_at 0.0003092 −5.8 ADH1B alcohol dehydrogenase IB (class 4q21-q23 I), beta polypeptide (ADH1B), mRNA. 209633_at 0.0006246 −2.2 PPP2R3A protein phosphatase 2 (formerly 3q22.1 2A), regulatory subunit B″, alpha (PPP2R3A), transcript variant 2, mRNA. 209657_s_at 0.0003701 −2.1 HSF2 heat shock transcription factor 2 6q22.31 (HSF2), mRNA. 209685_s_at 1.10E−05 3.7 PRKCB1 protein kinase C, beta 1 16p11.2 (PRKCB1), transcript variant 2, mRNA. 209733_at 1.64E−05 −2.7 LOC286440 Hypothetical protein Xq22.3 LOC286440 209737_at 0.0003955 −2.2 MAGI2 membrane associated guanylate 7q21 kinase, WW and PDZ domain containing 2 (MAGI2), mRNA. 209875_s_at 9.40E−06 9.5 SPP1 secreted phosphoprotein 1 4q21-q25 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1) (SPP1), mRNA. 209894_at 0.0001625 −4.2 LEPR leptin receptor (LEPR), 1p31 transcript variant 2, mRNA. 209897_s_at 0.0001202 2.5 SLIT2 slit homolog 2 (Drosophila) 4p15.2 (SLIT2), mRNA. 209969_s_at 1.51E−05 3.7 STAT1 signal transducer and activator 2q32.2 of transcription 1, 91 kDa (STAT1), transcript variant beta, mRNA. 210048_at 0.0008484 2.2 NAPG N-ethylmaleimide-sensitive 18p11.22 factor attachment protein, gamma (NAPG), mRNA. 210069_at 3.07E−05 2.8 CPT1B carnitine palmitoyltransferase 22q13.33 1B (muscle) (CPT1B), nuclear gene encoding mitochondrial protein, transcript variant 3, mRNA. 210365_at 0.0002181 2.6 RUNX1 Runt-related transcription factor 21q22.3 1 (acute myeloid leukemia 1; aml1 oncogene) 210438_x_at 0.0003684 −2.7 TROVE2 TROVE domain family, 1q31 member 2 (TROVE2), mRNA. 210621_s_at 0.0004078 −2.1 RASA1 RAS p21 protein activator 5q13.3 (GTPase activating protein) 1 (RASA1), transcript variant 2, mRNA. 210664_s_at 0.0006973 2.4 TFPI tissue factor pathway inhibitor 2q31-q32.1 (lipoprotein-associated coagulation inhibitor) (TFPI), transcript variant 1, mRNA. 210665_at 0.0003981 3.1 TFPI tissue factor pathway inhibitor 2q31-q32.1 (lipoprotein-associated coagulation inhibitor) (TFPI), transcript variant 2, mRNA. 210679_x_at 0.000265 3.4 BCL7A B-cell CLL/lymphoma 7A 12q24.13 210788_s_at 1.26E−05 −3.1 DHRS7 dehydrogenase/reductase (SDR 14q23.1 family) member 7 (DHRS7), mRNA. 210800_at 0.0009706 4.7 MGC12262 hypothetical protein MGC12262 210809_s_at 0.0002365 6.7 POSTN periostin, osteoblast specific 13q13.3 factor (POSTN), mRNA. 210944_s_at 0.0009253 2.3 CAPN3 calpain 3, (p94) (CAPN3), 15q15.1-q21.1 transcript variant 7, mRNA. 210950_s_at 1.38E−05 −3.3 FDFT1 farnesyl-diphosphate 8p23.1-p22 farnesyltransferase 1 (FDFT1), mRNA. 211040_x_at 0.0006364 2.4 GTSE1 G-2 and S-phase expressed 1 22q13.2-q13.3 (GTSE1), mRNA. 211276_at 8.52E−05 −5.6 TCEAL2 transcription elongation factor A Xq22.1-q22.3 (SII)-like 2 (TCEAL2), mRNA. 211423_s_at 0.000164 −2.8 SC5DL sterol-C5-desaturase (ERG3 11q23.3 delta-5-desaturase homolog, fungal)-like (SC5DL), transcript variant 1, mRNA. 211445_x_at 0.0007153 3.6 FKSG17 FKSG17 8q22.3 211452_x_at 5.23E−05 3.4 LRRFIP1 leucine rich repeat (in FLII) 2q37.3 interacting protein 1 (LRRFIP1), mRNA. 211454_x_at 0.0006917 3.7 211569_s_at 2.66E−05 −5.7 HADHSC L-3-hydroxyacyl-Coenzyme A 4q22-q26 dehydrogenase, short chain (HADHSC), mRNA. 211597_s_at 1.00E−07 13.1 HOP homeodomain-only protein 4q11-q12 (HOP), transcript variant 2, mRNA. 211623_s_at 0.0008386 −2.2 FBL fibrillarin (FBL), mRNA. 19q13.1 211666_x_at 9.60E−06 −2.6 RPL3 ribosomal protein L3 (RPL3), 22q13 mRNA. 211673_s_at 5.65E−05 3.5 MOCS1 Molybdenum cofactor synthesis 1 6p21.3 211710_x_at 0.0001136 −2.2 RPL4 ribosomal protein L4 (RPL4), 15q22 mRNA. 211725_s_at 0.0006346 2.4 BID BH3 interacting domain death 22q11.1 agonist (BID), transcript variant 3, mRNA. 211727_s_at 0.0004584 −2.5 COX11 COX11 homolog, cytochrome c 17q22 oxidase assembly protein (yeast) (COX11), nuclear gene encoding mitochondrial protein, mRNA. 211749_s_at 7.41E−05 −2.6 VAMP3 vesicle-associated membrane 1p36.23 protein 3 (cellubrevin) (VAMP3), mRNA. 211762_s_at 0.0002377 2.3 KPNA2 karyopherin alpha 2 (RAG 17q23.1-q23.3 cohort 1, importin alpha 1) (KPNA2), mRNA. 211769_x_at 4.67E−05 −2.4 TDE1 tumor differentially expressed 1 20q13.1-13.3 (TDE1), transcript variant 1, mRNA. 211813_x_at 1.69E−05 −4.8 DCN decorin (DCN), transcript 12q21.33 variant D, mRNA. 211896_s_at 0.0006287 −3.7 DCN decorin (DCN), transcript 12q21.33 variant C, mRNA. 211937_at 0.0001012 −3.2 EIF4B eukaryotic translation initiation 12q13.13 factor 4B (EIF4B), mRNA. 211938_at 3.00E−07 −3.2 EIF4B eukaryotic translation initiation 12q13.13 factor 4B (EIF4B), mRNA. 211941_s_at 2.01E−05 −2.3 PBP prostatic binding protein (PBP), 12q24.23 mRNA. 211942_x_at 7.02E−05 −2.8 RPL13A Ribosomal protein L13a 19q13.3 211964_at 0.0006935 3.4 COL4A2 Collagen, type IV, alpha 2 13q34 211980_at 0.0005493 3.9 COL4A1 collagen, type IV, alpha 1 13q34 (COL4A1), mRNA. 211986_at 3.42E−05 −3.3 AHNAK AHNAK nucleoprotein 11q12.2 (desmoyokin) (AHNAK), transcript variant 1, mRNA. 211988_at 1.30E−05 −2.2 SMARCE1 SWI/SNF related, matrix 17q21.2 associated, actin dependent regulator of chromatin, subfamily e, member 1 (SMARCE1), mRNA. 211994_at 0.0001256 −2 Transcribed locus, strongly 12 similar to XP_508919.1 PREDICTED: similar to protein kinase, lysine deficient 1; kinase deficient protein [Pan troglodytes] 211997_x_at 5.21E−05 −2.5 H3F3B H3 histone, family 3B (H3.3B) 17q25 (H3F3B), mRNA. 211998_at 7.80E−05 −3 H3F3B H3 histone, family 3B (H3.3B) 17q25 (H3F3B), mRNA. 212037_at 0.0001271 −2.7 PNN Pinin, desmosome associated 14q21.1 protein 212044_s_at 9.00E−07 3.4 RPL27A ribosomal protein L27a 11p15 (RPL27A), mRNA. 212052_s_at 0.0005363 2 KIAA0676 KIAA0676 protein 5q35.3 (KIAA0676), transcript variant 2, mRNA. 212094_at 0.0001189 −4.8 PEG10 PREDICTED: paternally 7 expressed 10 (PEG10), mRNA. 212096_s_at 0.0002831 −2.7 MTUS1 mitochondrial tumor suppressor 8p22 1 (MTUS1), nuclear gene encoding mitochondrial protein, transcript variant 5, mRNA. 212131_at 4.28E−05 −2 FAM61A family with sequence similarity 19q13.11 61, member A (FAM61A), mRNA. 212134_at 0.0003033 2 PHLDB1 pleckstrin homology-like 11q23.3 domain, family B, member 1 (PHLDB1), mRNA. 212144_at 0.0005431 −2.1 UNC84B unc-84 homolog B (C. elegans) 22q13.1 (UNC84B), mRNA. 212148_at 9.20E−06 −2.9 PBX1 Pre-B-cell leukemia 1q23 transcription factor 1 212151_at 0.0001748 −2.5 PBX1 Pre-B-cell leukemia 1q23 transcription factor 1 212171_x_at 0.0006474 3.3 VEGF vascular endothelial growth 6p12 factor (VEGF), transcript variant 6, mRNA. 212179_at 0.0003184 −2.5 C6orf111 Chromosome 6 open reading 6q16.3 frame 111 212188_at 0.000184 −2.9 KCTD12 potassium channel 13q22.3 tetramerisation domain containing 12 (KCTD12), mRNA. 212195_at 0.0002328 −2.1 IL6ST Interleukin 6 signal transducer 5q11 (gp130, oncostatin M receptor) 212199_at 0.0001637 −2.5 MRFAP1L1 Morf4 family associated protein 4p16.1 1-like 1 (MRFAP1L1), transcript variant 2, mRNA. 212215_at 0.0001021 −2.8 PREPL prolyl endopeptidase-like 2p22.1 (PREPL), mRNA. 212224_at 1.18E−05 −4.3 ALDH1A1 aldehyde dehydrogenase 1 9q21.13 family, member A1 (ALDH1A1), mRNA. 212236_x_at 0.0002768 5.3 KRT17 keratin 17 (KRT17), mRNA. 17q12-q21 212254_s_at 4.00E−06 −2.7 DST dystonin (DST), transcript 6p12-p11 variant 1eA, mRNA. 212256_at 0.0007645 −2.9 GALNT10 UDP-N-acetyl-alpha-D- 5q33.2 galactosamine:polypeptide N- acetylgalactosaminyltransferase 10 (GalNAc-T10) 212323_s_at 2.11E−05 2.5 VPS13D vacuolar protein sorting 13D 1p36.22-p36.21 (yeast) (VPS13D), transcript variant 2, mRNA. 212351_at 8.00E−06 2.2 EIF2B5 eukaryotic translation initiation 3q27.1 factor 2B, subunit 5 epsilon, 82 kDa (EIF2B5), mRNA. 212353_at 0.000225 3.6 SULF1 sulfatase 1 (SULF1), mRNA. 8q13.2-q13.3 212354_at 0.0002219 2.9 SULF1 sulfatase 1 (SULF1), mRNA. 8q13.2-q13.3 212365_at 0.0003347 4.1 MYO1B myosin IB (MYO1B), mRNA. 2q12-q34 212368_at 0.0002867 −2.3 ZNF292 PREDICTED: zinc finger 6 protein 292 (ZNF292), mRNA. 212408_at 1.41E−05 −2.6 TOR1AIP1 torsin A interacting protein 1 1q24.2 (TOR1AIP1), mRNA. 212413_at 0.0005848 2 6-Sep septin 6 (SEPT6), transcript Xq24 variant II, mRNA. 212414_s_at 0.0001527 2.4 6-Sep septin 6 (SEPT6), transcript Xq24 variant II, mRNA. 212435_at 0.0003489 −2.3 TRIM33 tripartite motif-containing 33 1p13.1 (TRIM33), transcript variant b, mRNA. 212468_at 0.0001247 −2 SPAG9 Sperm associated antigen 9 17q21.33 212498_at 1.50E−06 −2.7 MARCH-VI Membrane-associated ring 5p15.2 finger (C3HC4) 6 212510_at 0.0004844 −3.1 GPD1L glycerol-3-phosphate 3p24.1 dehydrogenase 1-like (GPD1L), mRNA. 212520_s_at 3.25E−05 3.1 SMARCA4 SWI/SNF related, matrix 19p13.2 associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4), mRNA. 212526_at 6.11E−05 −2.3 SPG20 spastic paraplegia 20, spartin 13q13.3 (Troyer syndrome) (SPG20), mRNA. 212549_at 6.64E−05 −2.4 STAT5B signal transducer and activator 17q11.2 of transcription 5B (STAT5B), mRNA. 212556_at 0.0003565 2.8 SCRIB scribbled homolog (Drosophila) 8q24.3 (SCRIB), transcript variant 2, mRNA. 212586_at 0.0004909 −2.1 CAST calpastatin (CAST), transcript 5q15-q21 variant 2, mRNA. 212595_s_at 0.0007053 −2 DAZAP2 DAZ associated protein 2 12q12 (DAZAP2), mRNA. 212609_s_at 1.85E−05 −2.4 AKT3 V-akt murine thymoma viral 1q43-q44 oncogene homolog 3 (protein kinase B, gamma) 212624_s_at 5.40E−06 6.9 CHN1 chimerin (chimaerin) 1 (CHN1), 2q31-q32.1 transcript variant 2, mRNA. 212632_at 0.0008287 −2 STX7 Syntaxin 7 6q23.1 212638_s_at 0.0007524 −2.2 WWP1 WW domain containing E3 8q21 ubiquitin protein ligase 1 (WWP1), mRNA. 212644_s_at 0.0001184 −2.3 C14orf32 chromosome 14 open reading 14q22.2-q22.3 frame 32 (C14orf32), mRNA. 212646_at 0.0003295 2.6 RAFTLIN raft-linking protein (RAFTLIN), 3p25.1-p24.3 mRNA. 212653_s_at 3.00E−07 −3.8 EHBP1 EH domain binding protein 1 2p15 (EHBP1), mRNA. 212675_s_at 0.0003318 −3.5 KIAA0582 KIAA0582 2p14 212730_at 0.0006706 −3.4 DMN desmuslin (DMN), transcript 15p26.3 variant B, mRNA. 212731_at 0.000105 −3.3 ANKRD46 ankyrin repeat domain 46 8q22.3 (ANKRD46), mRNA. 212751_at 0.0003336 −2.7 UBE2N ubiquitin-conjugating enzyme 12q22 E2N (UBC13 homolog, yeast) (UBE2N), mRNA. 212769_at 0.000184 2.7 TLE3 Transducin-like enhancer of 15q22 split 3 (E(sp1) homolog, Drosophila) 212776_s_at 0.0004769 −3 KIAA0657 PREDICTED: KIAA0657 2 protein (KIAA0657), mRNA. 212779_at 0.0005762 −2 KIAA1109 PREDICTED: hypothetical 4 protein KIAA1109 (KIAA1109), mRNA. 212798_s_at 3.32E−05 −2 ANKMY2 ankyrin repeat and MYND 7p21 domain containing 2 (ANKMY2), mRNA. 212809_at 7.32E−05 2.6 NFATC2IP nuclear factor of activated T- 16p11.2 cells, cytoplasmic, calcineurin- dependent 2 interacting protein (NFATC2IP), mRNA. 212841_s_at 0.0004662 2.6 PPFIBP2 PTPRF interacting protein, 11p15.4 binding protein 2 (liprin beta 2) (PPFIBP2), mRNA. 212943_at 0.0009511 −2.2 KIAA0528 KIAA0528 gene product 12p12.1 (KIAA0528), mRNA. 212971_at 0.0004892 2.2 CARS Cysteinyl-tRNA synthetase 11p15.5 213002_at 7.97E−05 3.8 MARCKS myristoylated alanine-rich 6q22.2 protein kinase C substrate (MARCKS), mRNA. 213005_s_at 0.0003887 −2.3 ANKRD15 ankyrin repeat domain 15 9p24.3 (ANKRD15), transcript variant 1, mRNA. 213027_at 0.0001503 −2.1 SSA2 TROVE domain family, 1q31 member 2 213029_at 6.18E−05 −2.4 NFIB Nuclear factor I/B 9p24.1 213047_x_at 0.0003826 −2.6 SET SET translocation (myeloid 9q34 leukemia-associated) (SET), mRNA. 213074_at 0.0002338 −2.6 PHIP Pleckstrin homology domain 6q14 interacting protein 213085_s_at 0.0005289 3.8 KIBRA KIBRA protein (KIBRA), 5q34 mRNA. 213093_at 1.80E−05 −2.8 PRKCA protein kinase C, alpha 17q22-q23.2 (PRKCA), mRNA. 213110_s_at 5.00E−06 −3.9 COL4A5 collagen, type IV, alpha 5 Xq22 (Alport syndrome) (COL4A5), transcript variant 1, mRNA. 213111_at 0.0006152 −2 PIP5K3 phosphatidylinositol-3- 2q34 phosphate/phosphatidylinositol 5-kinase, type III (PIP5K3), transcript variant 1, mRNA. 213117_at 0.0008783 −2 KLHL9 kelch-like 9 (Drosophila) 9p22 (KLHL9), mRNA. 213139_at 0.0008306 2.6 SNAI2 snail homolog 2 (Drosophila) 8q11 (SNAI2), mRNA. 213146_at 0.000125 2.9 KIAA0346 KIAA0346 protein 17p13.1 213224_s_at 0.0005954 −2 LOC92482 PREDICTED: hypothetical 10 protein LOC92482 (LOC92482), mRNA. 213227_at 0.0001677 −2 PGRMC2 Progesterone receptor membrane 4q26 component 2 213248_at 0.0006637 2.4 LOC221362 Hypothetical protein 6p12.3 LOC221362 213258_at 3.10E−05 2.5 TFPI Tissue factor pathway inhibitor 2q31-q32.1 (lipoprotein-associated coagulation inhibitor) 213272_s_at 6.80E−06 −4 LOC57146 promethin (LOC57146), mRNA. 16p12 213344_s_at 3.91E−05 2.7 H2AFX H2A histone family, member X 11q23.2-q23.3 (H2AFX), mRNA. 213350_at 1.20E−05 6.1 RPS11 ribosomal protein S11 (RPS11), 19q13.3 mRNA. 213364_s_at 4.00E−07 −3.7 SNX1 sorting nexin 1 (SNX1), 15q22.31 transcript variant 2, mRNA. 213370_s_at 0.0001347 2.1 SFMBT1 Scm-like with four mbt domains 3p21.1 1 (SFMBT1), transcript variant 3, mRNA. 213397_x_at 4.30E−06 −5.2 RNASE4 ribonuclease, RNase A family, 4 14q11.1 (RNASE4), transcript variant 3, mRNA. 213405_at 0.000663 −2.4 RAB22A RAB22A, member RAS 20q13.32 oncogene family (RAB22A), mRNA. 213413_at 0.000589 −2.4 SBLF stoned B-like factor (SBLF), 2p16.3 mRNA. 213418_at 3.79E−05 6.8 HSPA6 heat shock 70 kDa protein 6 1q23 (HSP70B′) (HSPA6), mRNA. 213464_at 0.0005718 2.7 SHC2 SHC (Src homology 2 domain 19p13.3 containing) transforming protein 2 213479_at 2.75E−05 4.3 NPTX2 neuronal pentraxin II (NPTX2), 7q21.3-q22.1 mRNA. 213523_at 5.86E−05 2.6 CCNE1 cyclin E1 (CCNE1), transcript 19q12 variant 2, mRNA. 213560_at 0.0005733 2.4 GADD45B growth arrest and DNA-damage- 19p13.3 inducible, beta (GADD45B), mRNA. 213574_s_at 1.00E−06 −2.4 KPNB1 Karyopherin (importin) beta 1 17q21.32 213605_s_at 0.0009961 2.5 FLJ40092 FLJ40092 protein 5q13.2 213661_at 8.00E−07 6.2 DKFZP586H2123 regeneration associated muscle 11p13 protease (DKFZP586H2123), transcript variant 2, mRNA. 213687_s_at 0.0009746 −2.1 RPL35A ribosomal protein L35a 3q29-qter (RPL35A), mRNA. 213693_s_at 7.45E−05 6.2 MUC1 mucin 1, transmembrane 1q21 (MUC1), transcript variant 4, mRNA. 213778_x_at 0.000467 2.2 ZFP276 zinc finger protein 276 homolog 16q24.3 (mouse) (ZFP276), mRNA. 213790_at 7.51E−05 4.4 ADAM12 A disintegrin and 10q26.3 metalloproteinase domain 12 (meltrin alpha) 213803_at p < 1e−07 −3.6 KPNB1 Karyopherin (importin) beta 1 17q21.32 213836_s_at 0.0001261 2.2 WIPI49 WD40 repeat protein Interacting 17q24.2 with phosphoInositides of 49 kDa (WIPI49), mRNA. 213848_at 2.00E−07 3.1 DUSP7 Dual specificity phosphatase 7 3p21 213869_x_at 0.0002103 4.6 THY1 Thy-1 cell surface antigen 11q22.3-q23 (THY1), mRNA. 213895_at 0.0004485 −2.5 EMP1 Epithelial membrane protein 1 12p12.3 213900_at 3.89E−05 −2.7 C9orf61 chromosome 9 open reading 9q13-q21 frame 61 (C9orf61), mRNA. 213905_x_at 0.0001976 4.6 BGN Biglycan Xq28 213943_at 4.00E−07 19 TWIST1 twist homolog 1 7p21.2 (acrocephalosyndactyly 3; Saethre-Chotzen syndrome) (Drosophila) (TWIST1), mRNA. 213979_s_at 0.0002226 3.3 CTBP1 C-terminal binding protein 1 4p16 (CTBP1), transcript variant 1, mRNA. 214023_x_at 0.000646 2.8 MGC8685 Tubulin, beta polypeptide 6p25 paralog 214041_x_at 0.000362 2.8 RPL37A Ribosomal protein L37a 2q35 214052_x_at 0.0005361 2.7 BAT2D1 BAT2 domain containing 1 1q23.3 (BAT2D1), mRNA. 214057_at 0.0005414 2.3 MCL1 myeloid cell leukemia sequence 1q21 1 (BCL2-related) (MCL1), transcript variant 2, mRNA. 214081_at 4.00E−07 10.2 PLXDC1 plexin domain containing 1 17q21.1 (PLXDC1), mRNA. 214097_at 2.29E−05 −2.3 RPS21 Ribosomal protein S21 20q13.3 214110_s_at 0.0001953 3 ESTs, Highly similar to A43542 lymphocyte-specific protein 1 [H. sapiens] 214140_at 0.0004058 2 SLC25A16 solute carrier family 25 10q21.3 (mitochondrial carrier; Graves disease autoantigen), member 16 (SLC25A16), nuclear gene encoding mitochondrial protein, mRNA. 214149_s_at 0.0003428 3.4 ATP6V0E ATPase, H+ transporting, 5q35.1 lysosomal 9 kDa, V0 subunit e 214177_s_at 0.0001027 −2.2 PBXIP1 pre-B-cell leukemia 1q22 transcription factor interacting protein 1 (PBXIP1), mRNA. 214264_s_at 0.0002244 2.1 C14orf143 chromosome 14 open reading 14q32.11 frame 143 (C14orf143), mRNA. 214316_x_at 7.97E−05 2.4 CALR Calreticulin 19p13.3-p13.2 214359_s_at 0.0001495 −3 HSPCB heat shock 90 kDa protein 1, beta 6p12 (HSPCB), mRNA. 214426_x_at 0.0008417 2.1 CHAF1A chromatin assembly factor 1, 19p13.3 subunit A (p150) (CHAF1A), mRNA. 214435_x_at 0.0005753 2.8 RALA v-ral simian leukemia viral 7p15-p13 oncogene homolog A (ras related) (RALA), mRNA. 214438_at 0.0009565 3.4 HLX1 H2.0-like homeo box 1 1q41-q42.1 (Drosophila) (HLX1), mRNA. 214527_s_at 4.20E−06 −2.3 PQBP1 polyglutamine binding protein 1 Xp11.23 (PQBP1), transcript variant 5, mRNA. 214594_x_at 0.0002968 2.9 ATP8B1 ATPase, Class I, type 8B, 18q21-q22 member 1 214707_x_at 0.0003366 2.8 ALMS1 Alstrom syndrome 1 2p13 214715_x_at 0.0002241 4.3 ZNF160 zinc finger protein 160 19q13.41 (ZNF160), transcript variant 1, mRNA. 214724_at 0.0006038 −2.1 DIXDC1 DIX domain containing 1 11q23.2 (DIXDC1), mRNA. 214737_x_at 0.0004018 −2.2 HNRPC heterogeneous nuclear 14q11.2 ribonucleoprotein C (C1/C2) (HNRPC), transcript variant 2, mRNA. 214855_s_at 4.03E−05 −2.6 GARNL1 GTPase activating Rap/RanGAP 14q13.2 domain-like 1 (GARNL1), transcript variant 2, mRNA. 214862_x_at 0.0009591 −2.8 MRNA; cDNA 10 DKFZp564G1162 (from clone DKFZp564G1162) 214924_s_at 2.90E−06 3.8 OIP106 OGT(O-Glc-NAc transferase)- 3p25.3-p24.1 interacting protein 106 KDa (OIP106), mRNA. 215016_x_at 1.50E−05 −2.3 DST dystonin (DST), transcript 6p12-p11 variant 1, mRNA. 215046_at 0.0006908 −2.2 FLJ23861 hypothetical protein FLJ23861 2q34 (FLJ23861), mRNA. 215073_s_at 3.83E−05 −2.1 NR2F2 nuclear receptor subfamily 2, 15q26 group F, member 2 (NR2F2), mRNA. 215076_s_at 0.000876 3 COL3A1 collagen, type III, alpha 1 2q31 (Ehlers-Danlos syndrome type IV, autosomal dominant) (COL3A1), mRNA. 215179_x_at 6.80E−05 4.5 PGF Placental growth factor, vascular 14q24-q31 endothelial growth factor-related protein 215203_at 0.0006265 2.2 GOLGA4 Golgi autoantigen, golgin 3p22-p21.3 subfamily a, 4 215206_at 0.0001618 3.1 EXT1 Exostoses (multiple) 1 8q24.11-q24.13 215208_x_at 0.0006292 3.4 RPL35A Ribosomal protein L35a 3q29-qter 215294_s_at 8.91E−05 −2.9 SMARCA1 SWI/SNF related, matrix Xq25 associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1), transcript variant 2, mRNA. 215306_at 0.0008848 −3.4 LHCGR Luteinizing 2p21 hormone/choriogonadotropin receptor 215336_at 9.25E−05 2.7 AKAP11 A kinase (PRKA) anchor protein 13q14.11 11 (AKAP11), transcript variant 2, mRNA. 215373_x_at 0.0004506 2.8 SET8 PR/SET domain containing 12q24.31 protein 8 215383_x_at 0.0009763 2.6 SPG21 Spastic paraplegia 21 15q21-q22 (autosomal recessive, Mast syndrome) 215404_x_at 0.0005104 3.2 FGFR1 Fibroblast growth factor 8p11.2-p11.1 receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome) 215467_x_at 0.0004682 3.9 DHX9 DEAH (Asp-Glu-Ala-His) box 1q25 polypeptide 9 215504_x_at 0.0006038 2.5 ANKRD10 Ankyrin repeat domain 10 13q34 215529_x_at 0.0007444 2.6 C21orf106 Chromosome 21 open reading 21q22.3 frame 106 215566_x_at 0.0007954 2.2 LYPLA2 lysophospholipase II (LYPLA2), 1p36.12-p35.1 mRNA. 215577_at 5.29E−05 2.4 UBE2E1 Ubiquitin-conjugating enzyme 3p24.2 E2E 1 (UBC4/5 homolog, yeast) 215588_x_at 6.38E−05 3.7 RIOK3 RIO kinase 3 (yeast) 18q11.2 215599_at 4.10E−06 3.9 SMA4 SMA4 5q13 215600_x_at 0.0005929 3.3 FBXW12 F-box and WD-40 domain 3p21.31 protein 12 215604_x_at 0.0003643 3.8 UBE2D2 Ubiquitin-conjugating enzyme 5q31.2 E2D 2 (UBC4/5 homolog, yeast) 215628_x_at 0.0005005 2.7 PPP2CA Protein phosphatase 2 (formerly 5q31.1 2A), catalytic subunit, alpha isoform 215978_x_at 9.04E−05 5.6 LOC152719 ATP-binding cassette, sub- 4p16.3 family A (ABC1), member 11 (pseudogene) 216035_x_at 0.000632 −2 TCF7L2 Transcription factor 7-like 2 (T- 10q25.3 cell specific, HMG-box) 216051_x_at 5.83E−05 5 KIAA1217 KIAA1217 10p12.31 216187_x_at 0.0001456 3.7 XRCC3 X-ray repair complementing 14q32.3 defective repair in Chinese hamster cells 3 216215_s_at 7.67E−05 −2.1 RBM9 RNA binding motif protein 9 22q13.1 216221_s_at 0.0007062 −2 PUM2 pumilio homolog 2 (Drosophila) 2p22-p21 (PUM2), mRNA. 216241_s_at 0.0005875 −2.1 TCEA1 transcription elongation factor A 8q11.2 (SII), 1 (TCEA1), transcript variant 2, mRNA. 216246_at 0.0004251 2.7 RPS20 ribosomal protein S20 (RPS20), 8q12 mRNA. 216274_s_at 0.0003437 −2.3 SEC11L1 SEC11-like 1 (S. cerevisiae) 15q25.3 (SEC11L1), mRNA. 216733_s_at 0.0005519 −3.3 GATM glycine amidinotransferase (L- 15q21.1 arginine:glycine amidinotransferase) (GATM), mRNA. 216858_x_at 0.0002005 4.1 216859_x_at 0.0004599 3.7 216944_s_at 0.0001923 −2.7 ITPR1 inositol 1,4,5-triphosphate 3p26-p25 receptor, type 1 (ITPR1), mRNA. 217028_at 0.000384 3.4 CXCR4 chemokine (C—X—C motif) 2q21 receptor 4 (CXCR4), transcript variant 2, mRNA. 217118_s_at 2.15E−05 2.2 C22orf9 chromosome 22 open reading 22q13.31 frame 9 (C22orf9), transcript variant 2, mRNA. 217466_x_at 0.0009002 −2.2 RPS2 Ribosomal protein S2 16p13.3 217497_at 0.0002299 3.3 ECGF1 Endothelial cell growth factor 1 22q13 (platelet-derived) 217579_x_at 0.0006875 2.5 ARL6IP2 ADP-ribosylation factor-like 6 2p22.2-p22.1 interacting protein 2 217586_x_at 0.000568 2.9 ESTs 217679_x_at 7.86E−05 4.8 ESTs, Weakly similar to hypothetical protein FLJ20489 [Homo sapiens] [H. sapiens] 217713_x_at 0.0001301 3.4 ESTs, Weakly similar to ALU6_HUMAN ALU SUBFAMILY SP SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 217715_x_at 0.0002336 3.9 ESTs 217773_s_at 0.0002007 −2.4 NDUFA4 NADH dehydrogenase 7p21.3 (ubiquinone) 1 alpha subcomplex, 4, 9 kDa (NDUFA4), nuclear gene encoding mitochondrial protein, mRNA. 217774_s_at 0.0007057 −2.1 HSPC152 hypothetical protein HSPC152 11q13.1 (HSPC152), mRNA. 217781_s_at 0.0003457 −2.5 ZFP106 zinc finger protein 106 homolog 15q15.1 (mouse) (ZFP106), mRNA. 217787_s_at 8.07E−05 2.7 GALNT2 UDP-N-acetyl-alpha-D- 1q41-q42 galactosamine:polypeptide N- acetylgalactosaminyltransferase 2 (GalNAc-T2) (GALNT2), mRNA. 217795_s_at 0.0001341 −2.1 TMEM43 transmembrane protein 43 3p25.1 (TMEM43), mRNA. 217814_at 0.0004705 −2.2 GK001 GK001 protein (GK001), 17q23.3 mRNA. 217833_at 0.000595 −2.5 SYNCRIP Synaptotagmin binding, 6q14-q15 cytoplasmic RNA interacting protein 217862_at 0.000351 −2.6 PIAS1 Protein inhibitor of activated 15q STAT, 1 217864_s_at 0.0004053 −2.2 PIAS1 protein inhibitor of activated 15q STAT, 1 (PIAS1), mRNA. 217888_s_at 0.0003955 2.2 ARFGAP1 ADP-ribosylation factor GTPase 20q13.33 activating protein 1 (ARFGAP1), transcript variant 1, mRNA. 217915_s_at 9.25E−05 −2.2 C15orf15 chromosome 15 open reading 15q21 frame 15 (C15orf15), mRNA. 217989_at 2.94E−05 −2.7 DHRS8 dehydrogenase/reductase (SDR 4q22.1 family) member 8 (DHRS8), mRNA. 217992_s_at 0.0003726 2.8 EFHD2 EF-hand domain family, 1p36.21 member D2 (EFHD2), mRNA. 218018_at 3.65E−05 2.2 PDXK pyridoxal (pyridoxine, vitamin 21q22.3 B6) kinase (PDXK), mRNA. 218025_s_at 2.20E−06 −4.3 PECI peroxisomal D3,D2-enoyl-CoA 6p24.3 isomerase (PECI), transcript variant 1, mRNA. 218031_s_at 4.00E−07 −4.3 CHES1 checkpoint suppressor 1 14q24.3-q32.11 (CHES1), mRNA. 218113_at 0.000146 2 TMEM2 transmembrane protein 2 9q13-q21 (TMEM2), mRNA. 218130_at 0.0004049 2 MGC4368 hypothetical protein MGC4368 17q25.3 (MGC4368), mRNA. 218131_s_at 2.87E−05 2.9 GATAD2A GATA zinc finger domain 19p13.11 containing 2A (GATAD2A), mRNA. 218151_x_at 0.0005594 2.2 GPR172A G protein-coupled receptor 8q24.3 172A (GPR172A), mRNA. 218155_x_at 0.000544 2.6 FLJ10534 hypothetical protein FLJ10534 17p13.3 (FLJ10534), mRNA. 218158_s_at 0.0001389 −2.7 APPL adaptor protein containing pH 3p21.1-p14.3 domain, PTB domain and leucine zipper motif 1 (APPL), mRNA. 218167_at 7.25E−05 −2.4 AMZ2 archaemetzincins-2 (AMZ2), 17q24.2 mRNA. 218191_s_at 6.81E−05 −2.8 LMBRD1 LMBR1 domain containing 1 6q13 (LMBRD1), mRNA. 218193_s_at 0.0002316 2.8 GOLT1B golgi transport 1 homolog B (S. cerevisiae) 12p12.1 (GOLT1B), mRNA. 218204_s_at 8.33E−05 −2.3 FYCO1 FYVE and coiled-coil domain 3p21.31 containing 1 (FYCO1), mRNA. 218311_at 0.0001916 −2.3 MAP4K3 mitogen-activated protein kinase 2p22.1 kinase kinase kinase 3 (MAP4K3), mRNA. 218373_at 0.0001922 −2.3 FTS fused toes homolog (mouse) 16q12.2 (FTS), transcript variant 2, mRNA. 218383_at 0.0003931 −2.7 C14orf94 chromosome 14 open reading 14q11.2 frame 94 (C14orf94), mRNA. 218432_at 0.0003175 −2.1 FBXO3 F-box protein 3 (FBXO3), 11p13 transcript variant 1, mRNA. 218450_at 0.0002984 −2.5 HEBP1 heme binding protein 1 12p13.1 (HEBP1), mRNA. 218504_at 0.0005544 −2 FAHD2A fumarylacetoacetate hydrolase 2p24.3-p11.2 domain containing 2A (FAHD2A), mRNA. 218528_s_at 4.23E−05 −2.3 RNF38 ring finger protein 38 (RNF38), 9p13-p12 transcript variant 4, mRNA. 218638_s_at 0.0008018 4 SPON2 spondin 2, extracellular matrix 4p16.3 protein (SPON2), mRNA. 218730_s_at 0.0002624 −6.8 OGN osteoglycin (osteoinductive 9q22 factor, mimecan) (OGN), transcript variant 3, mRNA. 218739_at 0.0002299 2.6 ABHD5 abhydrolase domain containing 3p21 5 (ABHD5), mRNA. 218804_at 1.58E−05 3.3 TMEM16A transmembrane protein 16A 11q13.3 (TMEM16A), mRNA. 218817_at 0.0005521 2 SPCS3 signal peptidase complex 4q34.2 subunit 3 homolog (S. cerevisiae) (SPCS3), mRNA. 218820_at 0.0007651 −3 C14orf132 chromosome 14 open reading 14q32.2 frame 132 (C14orf132), mRNA. 218831_s_at 7.99E−05 −2.6 FCGRT Fc fragment of IgG, receptor, 19q13.3 transporter, alpha (FCGRT), mRNA. 218856_at 2.20E−06 6.6 TNFRSF21 tumor necrosis factor receptor 6p21.1-12.2 superfamily, member 21 (TNFRSF21), mRNA. 218902_at 4.33E−05 2.5 NOTCH1 Notch homolog 1, translocation- 9q34.3 associated (Drosophila) (NOTCH1), mRNA. 218919_at 0.0001794 −3.1 ZFAND1 zinc finger, AN1-type domain 1 8q21.13 (ZFAND1), mRNA. 218929_at 3.34E−05 −2.1 CARF collaborates/cooperates with 4q35.1 ARF (alternate reading frame) protein (CARF), mRNA. 218961_s_at 0.0007861 2 PNKP polynucleotide kinase 3′- 19q13.3-q13.4 phosphatase (PNKP), mRNA. 219023_at 7.64E−05 −3.1 C4orf16 chromosome 4 open reading 4q25 frame 16 (C4orf16), mRNA. 219025_at 5.55E−05 4.3 CD248 CD248 antigen, endosialin 11q13 (CD248), mRNA. 219033_at 0.0007081 2.3 PARP8 poly (ADP-ribose) polymerase 5q11.1 family, member 8 (PARP8), mRNA. 219054_at 4.17E−05 −2.6 FLJ14054 hypothetical protein FLJ14054 5p13.3 (FLJ14054), mRNA. 219092_s_at 2.14E−05 2.2 C9orf12 chromosome 9 open reading 9q21.33-q22.31 frame 12 (C9orf12), mRNA. 219099_at 9.73E−05 2 C12orf5 chromosome 12 open reading 12p13.3 frame 5 (C12orf5), mRNA. 219102_at 1.21E−05 3 RCN3 reticulocalbin 3, EF-hand 19q13.33 calcium binding domain (RCN3), mRNA. 219105_x_at 9.00E−07 3.8 ORC6L origin recognition complex, 16q12 subunit 6 homolog-like (yeast) (ORC6L), mRNA. 219117_s_at 0.0002973 2.4 FKBP11 FK506 binding protein 11, 19 kDa 12q13.12 (FKBP11), mRNA. 219263_at 5.92E−05 4.2 RNF128 ring finger protein 128 Xq22.3 (RNF128), transcript variant 2, mRNA. 219279_at 0.0002023 2.7 DOCK10 dedicator of cytokinesis 10 2q36.3 (DOCK10), mRNA. 219289_at 0.0001862 2.3 FLJ20718 hypothetical protein FLJ20718 16q12.1 (FLJ20718), transcript variant 1, mRNA. 219290_x_at 0.0009817 3.8 DAPP1 dual adaptor of phosphotyrosine 4q25-q27 and 3-phosphoinositides (DAPP1), mRNA. 219358_s_at 1.60E−06 6.1 CENTA2 centaurin, alpha 2 (CENTA2), 17q11.2 mRNA. 219359_at 4.00E−06 4.4 FLJ22635 hypothetical protein FLJ22635 11p15.5 (FLJ22635), mRNA. 219368_at 0.0009624 −2.9 NAP1L2 nucleosome assembly protein 1- Xq13 like 2 (NAP1L2), mRNA. 219392_x_at 3.14E−05 4.3 FLJ11029 hypothetical protein FLJ11029 17q23.2 (FLJ11029), mRNA. 219407_s_at 0.0009809 4.1 LAMC3 laminin, gamma 3 (LAMC3), 9q31-q34 mRNA. 219449_s_at 0.0006528 −2.5 TMEM70 transmembrane protein 70 8q21.11 (TMEM70), mRNA. 219454_at 4.00E−07 36.8 EGFL6 EGF-like-domain, multiple 6 Xp22 (EGFL6), mRNA. 219493_at 0.0004597 2.6 SHCBP1 SHC SH2-domain binding 16q11.2 protein 1 (SHCBP1), mRNA. 219511_s_at 7.70E−06 −4.1 SNCAIP synuclein, alpha interacting 5q23.1-q23.3 protein (synphilin) (SNCAIP), mRNA. 219522_at 1.00E−07 7.7 FJX1 four jointed box 1 (Drosophila) 11p13 (FJX1), mRNA. 219549_s_at 0.0004199 −2.2 RTN3 reticulon 3 (RTN3), transcript 11q13 variant 4, mRNA. 219582_at 0.0004924 3 OGFRL1 opioid growth factor receptor- 6q13 like 1 (OGFRL1), mRNA. 219634_at 8.10E−06 3.8 CHST11 carbohydrate (chondroitin 4) 12q sulfotransferase 11 (CHST11), mRNA. 219641_at 0.0003308 −2.1 DET1 de-etiolated homolog 1 15q25.3 (Arabidopsis) (DET1), mRNA. 219700_at 1.10E−06 7.7 PLXDC1 plexin domain containing 1 17q21.1 (PLXDC1), mRNA. 219764_at 9.00E−07 6.7 FZD10 frizzled homolog 10 12q24.33 (Drosophila) (FZD10), mRNA. 219939_s_at 2.10E−06 −3.5 CSDE1 cold shock domain containing 1p22 E1, RNA-binding (CSDE1), transcript variant 2, mRNA. 219958_at 0.000873 3.2 C20orf46 chromosome 20 open reading 20p13 frame 46 (C20orf46), mRNA. 219961_s_at 0.0003792 −2.5 C20orf19 chromosome 20 open reading 20pter-q11.23 frame 19 (C20orf19), mRNA. 220014_at 1.38E−05 4.6 LOC51334 mesenchymal stem cell protein 5q23.1 DSC54 (LOC51334), mRNA. 220094_s_at 0.0002242 2 C6orf79 chromosome 6 open reading 6p24.3-p23 frame 79 (C6orf79), transcript variant 1, mRNA. 220113_x_at 0.0004047 3.1 POLR1B polymerase (RNA) I polypeptide 2q13 B, 128 kDa (POLR1B), mRNA. 220167_s_at 0.0008187 2 TP53TG3 TP53TG3 protein (TP53TG3), 16p13 transcript variant 2, mRNA. 220232_at 4.54E−05 4.8 SCD5 stearoyl-CoA desaturase 5 4q21.3 (SCD5), mRNA. 220242_x_at 0.0001347 2.2 ZNF701 zinc finger protein 701 19q13.41 (ZNF701), mRNA. 220266_s_at 1.44E−05 −3.3 KLF4 Kruppel-like factor 4 (gut) 9q31 (KLF4), mRNA. 220301_at 1.76E−05 5.8 C18orf14 chromosome 18 open reading 18q22.1 frame 14 (C18orf14), mRNA. 220327_at 8.86E−05 −2.7 VGL-3 vestigial-like 3 (VGL-3), 3p12.1 mRNA. 220334_at 0.0003043 3.1 RGS17 regulator of G-protein signalling 6q25.3 17 (RGS17), mRNA. 220432_s_at 0.000473 −3.2 CYP39A1 cytochrome P450, family 39, 6p21.1-p11.2 subfamily A, polypeptide 1 (CYP39A1), mRNA. 220575_at 4.48E−05 3.4 FLJ11800 hypothetical protein FLJ11800 17p11.2 (FLJ11800), mRNA. 220603_s_at 0.0001617 3.9 MCTP2 Multiple C2-domains with two 15q26.2 transmembrane regions 2 220720_x_at 0.0005432 3.3 FLJ14346 Hypothetical protein FLJ14346 2q21.1 220796_x_at 0.0002356 4.1 SLC35E1 Solute carrier family 35, 19p13.11 member E1 220817_at 4.50E−06 4.1 TRPC4 transient receptor potential 13q13.1-q13.2 cation channel, subfamily C, member 4 (TRPC4), mRNA. 220952_s_at 0.000293 −2.1 PLEKHA5 pleckstrin homology domain 12p12 containing, family A member 5 (PLEKHA5), mRNA. 220992_s_at 0.0003763 −2.1 C1orf25 Chromosome 1 open reading 1q25.2 frame 25 221012_s_at 0.0004784 2 TRIM8 tripartite motif-containing 8 10q24.3 (TRIM8), mRNA. 221059_s_at 2.20E−06 4.1 COTL1 coactosin-like 1 (Dictyostelium) 16q24.1 (COTL1), mRNA. 221127_s_at 0.000454 3.7 DKK3 dickkopf homolog 3 (Xenopus 11p15.2 laevis) (DKK3), transcript variant 3, mRNA. 221222_s_at 0.0005338 2.2 C1orf56 chromosome 1 open reading 1q21.2 frame 56 (C1orf56), mRNA. 221476_s_at 4.74E−05 −2.4 RPL15 ribosomal protein L15 (RPL15), 3p24.2 mRNA. 221486_at 0.0004058 −2 ENSA endosulfine alpha (ENSA), 1q21.2 transcript variant 7, mRNA. 221538_s_at 0.0004626 2.4 PLXNA1 plexin A1 (PLXNA1), mRNA. 3q21.3 221558_s_at 1.86E−05 4.6 LEF1 lymphoid enhancer-binding 4q23-q25 factor 1 (LEF1), mRNA. 221577_x_at 0.0006888 4.5 GDF15 growth differentiation factor 15 19p13.1-13.2 (GDF15), mRNA. 221588_x_at 0.0001441 −2.4 ALDH6A1 aldehyde dehydrogenase 6 14q24.3 family, member A1 (ALDH6A1), nuclear gene encoding mitochondrial protein, mRNA. 221589_s_at 1.20E−06 −4.3 ALDH6A1 Aldehyde dehydrogenase 6 14q24.3 family, member A1 221590_s_at 0.0008671 −2.3 ALDH6A1 Aldehyde dehydrogenase 6 14q24.3 family, member A1 221689_s_at 0.000155 −2 DSCR5 Down syndrome critical region 21q22.2 gene 5 (DSCR5), transcript variant 2, mRNA. 221691_x_at 1.46E−05 −3.2 NPM1 nucleophosmin (nucleolar 5q35 phosphoprotein B23, numatrin) (NPM1), mRNA. 221725_at 3.60E−05 −2.1 WASF2 WAS protein family, member 2 1p36.11-p34.3 221726_at 1.93E−05 −2.9 RPL22 ribosomal protein L22 (RPL22), 1p36.3-p36.2 mRNA. 221727_at 0.0001534 −2.3 PC4 Activated RNA polymerase II 5p13.3 transcription cofactor 4 221729_at 0.0004594 3.1 COL5A2 collagen, type V, alpha 2 2q14-q32 (COL5A2), mRNA. 221730_at 0.0007972 3.4 COL5A2 collagen, type V, alpha 2 2q14-q32 (COL5A2), mRNA. 221731_x_at 2.57E−05 10.4 CSPG2 chondroitin sulfate proteoglycan 5q14.3 2 (versican) (CSPG2), mRNA. 221747_at 0.0003412 −2.2 TNS Tensin 1 2q35-q36 221771_s_at 0.000498 −2.1 HSMPP8 M-phase phosphoprotein, mpp8 13q12.11 221840_at 0.0002221 3.2 PTPRE protein tyrosine phosphatase, 10q26 receptor type, E (PTPRE), transcript variant 2, mRNA. 221882_s_at 0.0003013 2.2 TMEM8 transmembrane protein 8 (five 16p13.3 membrane-spanning domains) (TMEM8), mRNA. 221943_x_at 0.0002266 2.4 RPL38 ribosomal protein L38 (RPL38), 17q23-q25 mRNA. 221988_at 1.59E−05 −2.3 MGC2747 Hypothetical protein MGC2747 19p13.11 222108_at 5.57E−05 −4.4 AMIGO2 adhesion molecule with Ig-like 12q13.11 domain 2 (AMIGO2), mRNA. 222207_x_at 0.0003362 3.2 CDNA: FLJ20949 fis, clone 7 ADSE01902 222212_s_at 0.0001439 −2.3 LASS2 LAG1 longevity assurance 1q21.2 homolog 2 (S. cerevisiae) (LASS2), transcript variant 3, mRNA. 222252_x_at 5.29E−05 4 LRRC51 leucine rich repeat containing 51 11q13.4 (LRRC51), mRNA. 222253_s_at 0.000969 4.6 DKFZP434P211 POM121-like protein 22q11.22 222358_x_at 7.05E−05 3.1 ESTs, Weakly similar to hypothetical protein FLJ20378 [Homo sapiens] [H. sapiens] 222372_at 0.0006654 2.5 BAIAP1 Membrane associated guanylate 3p14.1 kinase, WW and PDZ domain containing 1 222379_at 1.13E−05 3.5 KCNE4 Potassium voltage-gated 2q36.3 channel, Isk-related family, member 4 222394_at 1.44E−05 −2.8 PDCD6IP programmed cell death 6 3p23 interacting protein (PDCD6IP), mRNA. 222423_at 9.81E−05 −2.8 NDFIP1 Nedd4 family interacting protein 1 5q31.3 222431_at 0.0002108 −2.2 SPIN Spindlin 9q22.1-q22.3 222437_s_at 0.0006141 −2 VPS24 vacuolar protein sorting 24 2p24.3-p24.1 (yeast) (VPS24), transcript variant 2, mRNA. 222449_at 7.80E−06 4.1 TMEPAI transmembrane, prostate 20q13.31-q13.33 androgen induced RNA (TMEPAI), transcript variant 3, mRNA. 222453_at 4.19E−05 −2.7 CYBRD1 cytochrome b reductase 1 2q31.1 (CYBRD1), mRNA. 222482_at 1.85E−05 −2.4 SSBP3 Single stranded DNA binding 1p32.3 protein 3 222486_s_at 5.80E−06 −4.9 ADAMTS1 ADAM metallopeptidase with 21q21.2 thrombospondin type 1 motif, 1 (ADAMTS1), mRNA. 222488_s_at 9.10E−05 −2.4 DCTN4 dynactin 4 (p62) (DCTN4), 5q31-q32 mRNA. 222494_at 4.00E−06 −2.8 CHES1 checkpoint suppressor 1 14q24.3-q32.11 (CHES1), mRNA. 222503_s_at 0.0003949 2.5 WDR41 WD repeat domain 41 5q13.3 (WDR41), mRNA. 222533_at 0.0001299 −2.1 CRBN cereblon (CRBN), mRNA. 3p26.2 222538_s_at 0.0007304 −3.2 APPL adaptor protein containing pH 3p21.1-p14.3 domain, PTB domain and leucine zipper motif 1 (APPL), mRNA. 222605_at 1.64E−05 −3.1 RCOR3 REST corepressor 3 (RCOR3), 1q32.3 mRNA. 222722_at 1.25E−05 −8.7 OGN osteoglycin (osteoinductive 9q22 factor, mimecan) (OGN), transcript variant 3, mRNA. 222753_s_at 0.0001335 2.1 SPCS3 signal peptidase complex 4q34.2 subunit 3 homolog (S. cerevisiae) (SPCS3), mRNA. 222791_at 1.20E−06 −3.4 RSBN1 round spermatid basic protein 1 1p13.2 (RSBN1), mRNA. 222834_s_at 0.0006523 −2.1 GNG12 guanine nucleotide binding 1p31.2 protein (G protein), gamma 12 (GNG12), mRNA. 222968_at 5.98E−05 2.9 C6orf48 chromosome 6 open reading 6p21.3 frame 48 (C6orf48), mRNA. 222975_s_at 9.41E−05 −2.9 CSDE1 cold shock domain containing 1p22 E1, RNA-binding (CSDE1), transcript variant 2, mRNA. 223007_s_at 0.0007305 −2.7 C9orf5 chromosome 9 open reading 9q31 frame 5 (C9orf5), mRNA. 223010_s_at 0.0005426 −2.2 OCIAD1 OCIA domain containing 1 4p11 (OCIAD1), mRNA. 223011_s_at 0.0008498 −2 OCIAD1 OCIA domain containing 1 4p11 (OCIAD1), mRNA. 223050_s_at 0.0003276 2 FBXW5 F-box and WD-40 domain 9q34.3 protein 5 (FBXW5), transcript variant 1, mRNA. 223082_at 0.0003668 2.1 SH3KBP1 SH3-domain kinase binding Xp22.1-p21.3 protein 1 (SH3KBP1), transcript variant 1, mRNA. 223170_at 0.0001428 −2.6 DKFZP564K1964 DKFZP564K1964 protein 17q11.2 (DKFZP564K1964), mRNA. 223189_x_at 9.46E−05 −2.4 MLL5 myeloid/lymphoid or mixed- 7q22.1 lineage leukemia 5 (trithorax homolog, Drosophila) (MLL5), mRNA. 223208_at 0.0009547 2 KCTD10 potassium channel 12q24.11 tetramerisation domain containing 10 (KCTD10), mRNA. 223227_at 0.0006403 −2.2 BBS2 Bardet-Biedl syndrome 2 16q21 (BBS2), mRNA. 223263_s_at 0.0003743 −2.1 FGFR1OP2 FGFR1 oncogene partner 2 12p11.23 (FGFR1OP2), mRNA. 223276_at 5.10E−05 2.9 NID67 putative small membrane protein 5q33.1 NID67 (NID67), mRNA. 223283_s_at 0.0009337 −2.5 SDCCAG33 serologically defined colon 18q22.3 cancer antigen 33 (SDCCAG33), mRNA. 223306_at 6.02E−05 −2.4 EBPL emopamil binding protein-like 13q12-q13 (EBPL), mRNA. 223366_at 0.0008475 −2.9 CDNA FLJ16218 fis, clone 8 CTONG3001501, highly similar to Mus musculus glucocorticoid- induced gene 1 mRNA 223384_s_at 0.0009265 −2.1 TRIM4 tripartite motif-containing 4 7q22-q31.1 (TRIM4), transcript variant beta, mRNA. 223395_at 9.35E−05 −6.6 ABI3BP ABI gene family, member 3 3q12 (NESH) binding protein (ABI3BP), mRNA. 223437_at 0.0004419 −2.2 PPARA peroxisome proliferative 22q13.31 activated receptor, alpha (PPARA), transcript variant 3, mRNA. 223464_at 0.0004952 2.3 OSBPL5 oxysterol binding protein-like 5 11p15.4 (OSBPL5), transcript variant 2, mRNA. 223501_at 0.0004401 4.3 TNFSF13B Tumor necrosis factor (ligand) 13q32-34 superfamily, member 13b 223538_at 0.0008098 2 SERF1A Small EDRK-rich factor 1A 5q12.2-q13.3 (telomeric) 223566_s_at 0.0007174 −2.7 BCOR BCL6 co-repressor (BCOR), Xp21.2-p11.4 transcript variant 1, mRNA. 223617_x_at 3.01E−05 2.6 ATAD3B ATPase family, AAA domain 1p36.33 containing 3B (ATAD3B), mRNA. 223629_at 0.0008805 −2.4 PCDHB5 protocadherin beta 5 5q31 (PCDHB5), mRNA. 223672_at 0.0001002 4.8 SGIP1 SH3-domain GRB2-like 1p31.2 (endophilin) interacting protein 1 (SGIP1), mRNA. 223697_x_at 0.0001465 4.6 C9orf64 chromosome 9 open reading 9q21.32 frame 64 (C9orf64), mRNA. 223991_s_at 2.42E−05 2.6 GALNT2 UDP-N-acetyl-alpha-D- 1q41-q42 galactosamine:polypeptide N- acetylgalactosaminyltransferase 2 (GalNAc-T2) (GALNT2), mRNA. 224254_x_at 2.71E−05 5.5 TF Transferrin 3q22.1 224445_s_at 1.11E−05 −3 ZFYVE21 zinc finger, FYVE domain 14q32.33 containing 21 (ZFYVE21), mRNA. 224549_x_at 6.50E−06 8 224598_at 3.68E−05 2.4 MGAT4B mannosyl (alpha-1,3-)- 5q35 glycoprotein beta-1,4-N- acetylglucosaminyltransferase, isoenzyme B (MGAT4B), transcript variant 1, mRNA. 224605_at 0.0002548 −2.2 LOC401152 HCV F-transactivated protein 1 4q26 (LOC401152), mRNA. 224612_s_at 6.79E−05 2.2 DNAJC5 DnaJ (Hsp40) homolog, 20q13.33 subfamily C, member 5 224618_at 0.0001475 2 ROD1 ROD1 regulator of 9q32 differentiation 1 (S. pombe) 224660_at 0.0008567 −2.1 MGC14156 hypothetical protein MGC14156 4q22.1 (MGC14156), mRNA. 224664_at 0.0003695 −2.3 C10orf104 chromosome 10 open reading 10q22.1 frame 104 (C10orf104), mRNA. 224665_at 0.0004075 −2.2 C10orf104 chromosome 10 open reading 10q22.1 frame 104 (C10orf104), mRNA. 224667_x_at 0.0002844 3.1 Transcribed locus 224689_at 0.0001149 −2 MANBAL mannosidase, beta A, lysosomal- 20q11.23-q12 like (MANBAL), transcript variant 2, mRNA. 224734_at 0.0001511 −2.9 HMGB1 High-mobility group box 1 13q12 224741_x_at 0.0001144 −2.5 GAS5 Growth arrest-specific 5 1q23.3 224754_at 0.000206 −2.2 SP1 Sp1 transcription factor (SP1), 12q13.1 mRNA. 224755_at 0.0001441 −2.2 SMBP SM-11044 binding protein 10q24.1 224763_at 5.30E−06 −3.9 RPL37 ribosomal protein L37 (RPL37), 5p13 mRNA. 224780_at 0.0008827 −2 RBM17 RNA binding motif protein 17 10p15.1 (RBM17), mRNA. 224812_at 0.0001992 −2.3 HIBADH 3-hydroxyisobutyrate 7p15.2 dehydrogenase (HIBADH), mRNA. 224841_x_at 0.0001078 −2.6 RNU47 PREDICTED: RNA, U47 small 1 nuclear (RNU47), misc RNA. 224856_at 0.0004439 −2.6 FKBP5 FK506 binding protein 5 6p21.3-21.2 (FKBP5), mRNA. 224893_at 0.0003585 −2.8 DKFZP564J0863 DKFZP564J0863 protein 11q13.1 224895_at 0.000307 −2.6 YAP1 Yes-associated protein 1, 65 kDa 11q13 (YAP1), mRNA. 224901_at 1.70E−05 −3.5 SCD4 Stearoyl-CoA desaturase 5 4q21.3 224950_at 0.0009862 2.2 PTGFRN prostaglandin F2 receptor 1p13.1 negative regulator (PTGFRN), mRNA. 224967_at 5.98E−05 2.7 UGCG UDP-glucose ceramide 9q31 glucosyltransferase 224970_at 5.88E−05 −2.5 NFIA Nuclear factor I/A 1p31.3-p31.2 225050_at 4.85E−05 −2.5 ZNF512 zinc finger protein 512 2p23 (ZNF512), mRNA. 225060_at 0.0001496 −2.4 LRP11 low density lipoprotein receptor- 6q25.1 related protein 11 (LRP11), mRNA. 225078_at 0.0002343 −3.4 EMP2 Epithelial membrane protein 2 16p13.2 225098_at 0.0001021 −2 ABI2 Abl interactor 2 2q33 225106_s_at 0.0005784 2.9 FLJ10826 hypothetical protein FLJ10826 16q12.2 (FLJ10826), transcript variant 2, mRNA. 225123_at 4.00E−07 −3.1 SESN3 Sestrin 3 11q21 225125_at 3.50E−05 −3.1 TMEM32 transmembrane protein 32 Xq26.3 (TMEM32), mRNA. 225132_at 0.0001306 −2 FBXL3 F-box and leucine-rich repeat 13q22 protein 3 (FBXL3), mRNA. 225133_at 4.79E−05 −2.6 KLF3 Kruppel-like factor 3 (basic) 4p14 225147_at 1.50E−06 3.7 PSCD3 pleckstrin homology, Sec7 and 7p22.1 coiled-coil domains 3 (PSCD3), mRNA. 225162_at 1.40E−05 −3.8 SH3D19 SH3 domain protein D19 4q31.3 (SH3D19), mRNA. 225179_at 0.0001313 −2.1 HIP2 Huntingtin interacting protein 2 4p14 225198_at 2.56E−05 −2.7 VAPA VAMP (vesicle-associated 18p11.22 membrane protein)-associated protein A, 33 kDa (VAPA), transcript variant 2, mRNA. 225207_at 0.0001018 −3.4 PDK4 pyruvate dehydrogenase kinase, 7q21.3-q22.1 isoenzyme 4 (PDK4), mRNA. 225219_at 2.70E−05 −3.5 SMAD5 SMAD, mothers against DPP 5q31 homolog 5 (Drosophila) (SMAD5), transcript variant 3, mRNA. 225220_at 0.00074 −2.2 Homo sapiens, clone 4 IMAGE: 4249217, mRNA 225223_at 2.89E−05 −2 SMAD5 SMAD, mothers against DPP 5q31 homolog 5 (Drosophila) (SMAD5), transcript variant 3, mRNA. 225239_at 0.0004432 4.3 Immunoglobulin light chain 11 variable region 225243_s_at 0.0001227 −2.6 SLMAP sarcolemma associated protein 3p21.2-p14.3 (SLMAP), mRNA. 225274_at 2.80E−06 −3 SNRPG Small nuclear ribonucleoprotein 2p13.3 polypeptide G 225310_at 0.000177 −2.2 RBMX RNA binding motif protein, X- Xq26.3 linked 225326_at 8.88E−05 −2 RBM27 PREDICTED: RNA binding 5 motif protein 27 (RBM27), mRNA. 225330_at 0.0002697 −2.1 IGF1R Insulin-like growth factor 1 15q26.3 receptor 225332_at 5.78E−05 −2.1 KRTAP4-7 Keratin associated protein 4-7 17q12-q21 225344_at 0.0004132 2.8 NCOA7 nuclear receptor coactivator 7 6q22.32 (NCOA7), mRNA. 225352_at 0.0001828 −2.3 TLOC1 translocation protein 1 3q26.2 (TLOC1), mRNA. 225381_at 0.0006635 −4.3 LOC399959 PREDICTED: hypothetical 11 LOC399959 (LOC399959), mRNA. 225387_at 3.43E−05 −3.2 TM4SF9 Tetraspanin 5 4q23 225416_at 0.0003496 −2.2 RNF12 Ring finger protein 12 Xq13-q21 225421_at 0.0009226 −3.1 ACY1L2 aminoacylase 1-like 2 6q15 (ACY1L2), mRNA. 225426_at 6.78E−05 −2.5 PPP6C Protein phosphatase 6, catalytic 9q33.3 subunit 225480_at 0.0002718 2.2 C1orf122 chromosome 1 open reading 1p34.3 frame 122 (C1orf122), mRNA. 225489_at 3.71E−05 −2 TMEM18 transmembrane protein 18 2p25.3 (TMEM18), mRNA. 225498_at 7.45E−05 −2.2 CHMP4B chromatin modifying protein 4B 20q11.22 (CHMP4B), mRNA. 225505_s_at 1.90E−06 4.1 C20orf81 chromosome 20 open reading 20p13 frame 81 (C20orf81), mRNA. 225509_at 1.01E−05 −2.9 SAP30L Hypothetical protein LOC56757 5q33.2 225524_at 5.00E−05 −3.1 ANTXR2 anthrax toxin receptor 2 4q21.21 (ANTXR2), mRNA. 225526_at 0.0004149 −2 MKLN1 muskelin 1, intracellular 7q32 mediator containing kelch motifs (MKLN1), mRNA. 225546_at 4.45E−05 −2.7 EEF2K Eukaryotic elongation factor-2 16p12.1 kinase 225571_at 0.000188 −4.7 LIFR leukemia inhibitory factor 5p13-p12 receptor (LIFR), mRNA. 225574_at 8.57E−05 −2.4 MGC10198 hypothetical protein MGC10198 4q35.1 (MGC10198), mRNA. 225575_at 0.0003237 −4.5 LIFR leukemia inhibitory factor 5p13-p12 receptor (LIFR), mRNA. 225611_at 0.0004119 −2.6 MAST4 Microtubule associated 5q12.3 serine/threonine kinase family member 4 225626_at 0.0003153 4.8 PAG1 phosphoprotein associated with 8q21.13 glycosphingolipid microdomains 1 (PAG1), mRNA. 225636_at 0.000278 2.5 STAT2 signal transducer and activator 12q13.3 of transcription 2, 113 kDa (STAT2), mRNA. 225646_at 1.50E−05 4.4 CTSC cathepsin C (CTSC), transcript 11q14.1-q14.3 variant 2, mRNA. 225647_s_at 0.0009077 2.5 CTSC cathepsin C (CTSC), transcript 11q14.1-q14.3 variant 1, mRNA. 225686_at 0.0003333 2.2 FAM33A family with sequence similarity 17q23.2 33, member A (FAM33A), mRNA. 225698_at 3.41E−05 −3.2 TIGA1 TIGA1 (TIGA1), mRNA. 5q21-q22 225728_at 0.0006083 −2.8 ARGBP2 Arg/Abl-interacting protein 4q35.1 ArgBP2 225793_at 0.000103 −2.1 MGC46719 Lix1 homolog (mouse) like 1q21.1 225799_at 2.29E−05 5.2 MGC4677 hypothetical protein MGC4677 2p11.2 (MGC4677), mRNA. 225811_at 5.44E−05 −2.1 Transcribed locus, weakly 11 similar to XP_510104.1 PREDICTED: similar to hypothetical protein FLJ25224 [Pan troglodytes] 225845_at 0.0003774 −3.4 BTBD15 BTB (POZ) domain containing 11q24.3 15 (BTBD15), mRNA. 225855_at 7.78E−05 −2.4 EPB41L5 erythrocyte membrane protein 2q14.2 band 4.1 like 5 (EPB41L5), mRNA. 225886_at 0.0005086 −2.2 DDX5 RNA-binding protein 45 17q21 (RBP45), putative 225915_at 3.50E−05 −3.4 CAB39L Calcium binding protein 39-like 13q14.2 225939_at 0.0001338 −2.8 EIF4E3 Eukaryotic translation initiation 3p14 factor 4E member 3 225941_at 0.0002862 −2.2 EIF4E3 Eukaryotic translation initiation 3p14 factor 4E member 3 225946_at 0.0003511 −2.3 C12orf2 Chromosome 12 open reading 12p12.3 frame 2 225947_at 5.75E−05 2.3 MYOHD1 myosin head domain containing 17q12 1 (MYOHD1), mRNA. 225967_s_at 0.0001375 2.5 LOC284184 PREDICTED: hypothetical 17 LOC284184 (LOC284184), mRNA. 225976_at 0.0003271 −2 BTF3L4 basic transcription factor 3-like 1p32.3 4 (BTF3L4), mRNA. 225987_at 0.0003503 3.3 TNFAIP9 STEAP family member 4 7q21.12 225996_at 0.0006306 −9.3 MRNA; cDNA 2 DKFZp686N1345 (from clone DKFZp686N1345) 226017_at 0.000301 2.3 CKLFSF7 chemokine-like factor 3p23 superfamily 7 (CKLFSF7), transcript variant 2, mRNA. 226020_s_at 7.89E−05 −2.2 OMA1 OMA1 homolog, zinc 1p32.2-p32.1 metallopeptidase (S. cerevisiae) (OMA1), mRNA. 226038_at 0.0002389 −3.2 LONRF1 LON peptidase N-terminal 8p23.1 domain and ring finger 1 (LONRF1), mRNA. 226063_at 4.00E−06 3.3 VAV2 vav 2 oncogene (VAV2), 9q34.1 mRNA. 226066_at 0.0005179 −3 MITF microphthalmia-associated 3p14.2-p14.1 transcription factor (MITF), transcript variant 5, mRNA. 226117_at 8.72E−05 −2.7 TIFA TRAF-interacting protein with a 4q25 forkhead-associated domain (TIFA), mRNA. 226120_at 0.0001436 −2.7 TTC8 tetratricopeptide repeat domain 14q31.3 8 (TTC8), transcript variant 3, mRNA. 226180_at 0.0009691 −2 WDR36 WD repeat domain 36 5q22.1 (WDR36), mRNA. 226184_at 3.75E−05 −3.6 FMNL2 formin-like 2 (FMNL2), 2q23.3 transcript variant 2, mRNA. 226203_at 0.0003968 −2 CDNA clone IMAGE: 5299888 15 226223_at 0.0002488 −2.6 PAWR PRKC, apoptosis, WT1, 12q21 regulator 226225_at 0.0003786 −3.2 MCC Mutated in colorectal cancers 5q21-q22 226230_at 0.0002589 −2.4 KIAA1387 KIAA1387 protein 2p16.1 226280_at 3.34E−05 −2.8 BNIP2 BCL2/adenovirus E1B 19 kDa 15q22.2 interacting protein 2 226297_at 8.43E−05 −2.1 ESTs 226303_at 0.0003656 −2.9 PGM5 phosphoglucomutase 5 (PGM5), 9q13 mRNA. 226336_at 0.0001456 −2 PPIA Peptidylprolyl isomerase A 7p13-p11.2 (cyclophilin A) 226344_at 0.0009627 −2.9 ZMAT1 zinc finger, matrin type 1 Xq21 (ZMAT1), transcript variant 1, mRNA. 226403_at 9.20E−06 3.8 TMC4 transmembrane channel-like 4 19q13.42 (TMC4), mRNA. 226472_at 0.0007652 −2 PPIL4 peptidylprolyl isomerase 6q24-q25 (cyclophilin)-like 4 (PPIL4), mRNA. 226484_at 0.0009077 2 ZNF651 zinc finger protein 651 3p22.1 (ZNF651), mRNA. 226499_at 0.0009453 2.8 MGC61598 Similar to ankyrin-repeat protein 9q34.3 Nrarp 226521_s_at 0.0006084 −2.1 FLJ13614 hypothetical protein FLJ13614 4q21.21-q21.23 (FLJ13614), mRNA. 226529_at 4.85E−05 −2.3 FLJ11273 hypothetical protein FLJ11273 7p21.3 (FLJ11273), mRNA. 226541_at 0.0001172 −2.3 FBXO30 F-box protein 30 (FBXO30), 6q24 mRNA. 226561_at 0.0006025 −2.1 LOC285086 Hypothetical protein 2q36.3 LOC285086 226599_at 0.0002151 2.3 KIAA1727 KIAA1727 protein 4q31.3 (KIAA1727), mRNA. 226625_at 7.30E−06 −3.8 TGFBR3 Transforming growth factor, 1p33-p32 beta receptor III (betaglycan, 300 kDa) 226663_at 8.60E−06 2.8 ANKRD10 Ankyrin repeat domain 10 13q34 226668_at 0.0003707 −2.6 WDSUB1 WD repeat, SAM and U-box 2q24.2 domain containing 1 (WDSUB1), mRNA. 226688_at 0.0002101 −3.3 C3orf23 chromosome 3 open reading 3p21.33-p21.32 frame 23 (C3orf23), transcript variant 1, mRNA. 226695_at 0.0001301 2.5 PRRX1 paired related homeobox 1 1q24 (PRRX1), transcript variant pmx-1b, mRNA. 226705_at 0.0002111 −2 FGFR1 Fibroblast growth factor 8p11.2-p11.1 receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome) 226713_at 1.81E−05 −2.9 C3orf6 Chromosome 3 open reading 3 frame 6 226747_at 0.0006894 −3.7 KIAA1344 KIAA1344 (KIAA1344), 14q22.1 mRNA. 226751_at 8.30E−06 −2.4 C2orf32 chromosome 2 open reading 2p14 frame 32 (C2orf32), mRNA. 226765_at 0.0002842 2.2 SPTBN1 Spectrin, beta, non-erythrocytic 1 2p21 226777_at 5.39E−05 4.9 ADAM12 A disintegrin and 10q26.3 metalloproteinase domain 12 (meltrin alpha) 226806_s_at 1.95E−05 −2.8 MRNA; cDNA 1 DKFZp686J23256 (from clone DKFZp686J23256) 226829_at 0.0006675 2.9 KIAA1914 KIAA1914 (KIAA1914), 10q25.3 transcript variant 2, mRNA. 226867_at 0.0008554 −2 C9orf55 Chromosome 9 open reading 9p22.1 frame 55 226873_at 0.0002067 −2.8 Transcribed locus 16 226899_at 3.10E−06 3.1 UNC5B unc-5 homolog B (C. elegans) 10q22.1 (UNC5B), mRNA. 226909_at 0.0004528 −2 KIAA1729 KIAA1729 protein 4p16.1 (KIAA1729), mRNA. 226911_at 1.20E−05 3.7 FLJ39155 hypothetical protein FLJ39155 5p13.2-p13.1 (FLJ39155), transcript variant 4, mRNA. 226933_s_at 5.79E−05 3.8 ID4 inhibitor of DNA binding 4, 6p22-p21 dominant negative helix-loop- helix protein (ID4), mRNA. 226943_at 0.0004664 2 MRNA; cDNA DKFZp547P055 12 (from clone DKFZp547P055) 226994_at 0.0002644 −2.3 DNAJA2 DnaJ (Hsp40) homolog, 16q11.1-q11.2 subfamily A, member 2 226997_at 0.0002372 3.7 CDNA FLJ10196 fis, clone 5 HEMBA1004776 227031_at 0.0001825 −2.4 SNX13 Sorting nexin 13 7p21.1 227070_at 0.0003008 −2.7 GLT8D2 glycosyltransferase 8 domain 12q containing 2 (GLT8D2), mRNA. 227082_at 0.0007234 −2 MRNA; cDNA 3 DKFZp586K1922 (from clone DKFZp586K1922) 227121_at 0.0006088 −2.1 MRNA; cDNA 3 DKFZp586K1922 (from clone DKFZp586K1922) 227132_at 0.0002728 −2.4 LOC51123 HSPC038 protein (LOC51123), 8q22.3 mRNA. 227138_at 0.0008198 −2.1 CRTAP cartilage associated protein 3p22.3 (CRTAP), mRNA. 227148_at 0.0001511 −3.4 PLEKHH2 pleckstrin homology domain 2p21 containing, family H (with MyTH4 domain) member 2 (PLEKHH2), mRNA. 227178_at 0.0005124 −3.9 CUGBP2 CUG triplet repeat, RNA 10p13 binding protein 2 (CUGBP2), transcript variant 2, mRNA. 227197_at 0.000108 −2.9 SGEF Src homology 3 domain- 3q25.2 containing guanine nucleotide exchange factor 227214_at 0.0002058 2.1 GOPC Golgi associated PDZ and 6q21 coiled-coil motif containing 227221_at 0.0004345 2.1 CDNA FLJ31683 fis, clone 3 NT2RI2005353 227260_at 0.0001678 3 Transcribed locus 1 227273_at 4.47E−05 −2.6 Transcribed locus 10 227278_at 0.0005386 2.3 Transcribed locus, weakly 1 similar to XP_510104.1 PREDICTED: similar to hypothetical protein FLJ25224 [Pan troglodytes] 227293_at 8.47E−05 −2.2 LNX Ligand of numb-protein X 4q12 227295_at 2.70E−06 3.4 IKIP IKK interacting protein (IKIP), 12q23.1 transcript variant 3.1, mRNA. 227317_at 0.0003721 2.3 LMCD1 LIM and cysteine-rich domains 3p26-p24 1 (LMCD1), mRNA. 227347_x_at 2.86E−05 4 HES4 hairy and enhancer of split 4 1p36.33 (Drosophila) (HES4), mRNA. 227372_s_at 0.0004102 3.4 BAIAP2L1 BAI1-associated protein 2-like 1 7q21.3-q22.1 (BAIAP2L1), mRNA. 227383_at 0.0005636 2.4 Similar to KIAA0454 protein 1q21.1 227384_s_at 0.000128 2.6 Similar to KIAA0454 protein 1q21.1 227396_at 0.0001476 2.6 Homo sapiens, clone 11 IMAGE: 4454331, mRNA 227407_at 9.42E−05 −2.3 FLJ90013 hypothetical protein FLJ90013 4p15.32 (FLJ90013), mRNA. 227529_s_at 0.0001731 −2.9 AKAP12 A kinase (PRKA) anchor protein 6q24-q25 (gravin) 12 227530_at 8.47E−05 −3 AKAP12 A kinase (PRKA) anchor protein 6q24-q25 (gravin) 12 227636_at 0.0003391 −2.3 THAP5 THAP domain containing 5 7q31.1 227703_s_at 1.29E−05 −5.9 SYTL4 synaptotagmin-like 4 Xq21.33 (granuphilin-a) (SYTL4), mRNA. 227708_at 0.0006098 −2.1 EEF1A1 Eukaryotic translation 6q14.1 elongation factor 1 alpha 1 227719_at 4.00E−06 −3.6 CDNA FLJ37828 fis, clone 13 BRSSN2006575 227728_at 6.11E−05 −2.9 PPM1A Protein phosphatase 1A 14q23.1 (formerly 2C), magnesium- dependent, alpha isoform 227827_at 0.0008248 −4.5 ARGBP2 Arg/Abl-interacting protein 4q35.1 ArgBP2 227850_x_at 0.0001134 2.9 CDC42EP5 CDC42 effector protein (Rho 19q13.42 GTPase binding) 5 (CDC42EP5), mRNA. 227866_at 0.0007379 −2 RBM16 RNA binding motif protein 16 6q25.1-q25.3 227945_at 0.0003107 −2.3 TBC1D1 TBC1 (tre-2/USP6, BUB2, 4p14 cdc16) domain family, member 1 (TBC1D1), mRNA. 227952_at 0.0001513 4.1 Full length insert cDNA clone 4 YI46G04 227971_at 3.26E−05 −4.1 NRK Nik related kinase (NRK), Xq22.3 mRNA. 228012_at 0.0006848 −2 MATR3 Matrin 3 5q31.2 228027_at 3.77E−05 −4 GPRASP2 G protein-coupled receptor Xq22.1 associated sorting protein 2 (GPRASP2), transcript variant 2, mRNA. 228030_at 0.0005637 3 RBM6 RNA binding motif protein 6 3p21.3 228098_s_at 0.0009902 2.2 MYLIP myosin regulatory light chain 6p23-p22.3 interacting protein (MYLIP), mRNA. 228202_at 0.0001345 −9.3 PLN Phospholamban 6q22.1 228204_at 1.00E−07 2.9 PSMB4 proteasome (prosome, 1q21 macropain) subunit, beta type, 4 (PSMB4), mRNA. 228253_at 1.10E−05 3.8 LOXL3 lysyl oxidase-like 3 (LOXL3), 2p13 mRNA. 228297_at 0.0004293 3.3 CNN3 calponin 3, acidic (CNN3), 1p22-p21 mRNA. 228310_at 8.10E−06 −3.3 ENAH enabled homolog (Drosophila) 1q42.12 (ENAH), transcript variant 2, mRNA. 228331_at 0.0002123 3.4 C11orf31 Chromosome 11 open reading 11q12.1 frame 31 228333_at 0.0005407 −2.2 Full length insert cDNA clone 2 YT94E02 228335_at 0.0008785 −3.8 CLDN11 claudin 11 (oligodendrocyte 3q26.2-q26.3 transmembrane protein) (CLDN11), mRNA. 228497_at 0.0001644 3.2 SLC22A15 solute carrier family 22 (organic 1p13.1 cation transporter), member 15 (SLC22A15), mRNA. 228523_at 0.0004047 2 NANOS1 nanos homolog 1 (Drosophila) 10q26.11 (NANOS1), transcript variant 2, mRNA. 228551_at 3.95E−05 −3.1 MGC24039 Hypothetical protein 12p11.21 MGC24039 228554_at 1.35E−05 −4.7 MRNA; cDNA 11 DKFZp586G0321 (from clone DKFZp586G0321) 228569_at 0.0006815 −2.2 PAPOLA Poly(A) polymerase alpha 14q32.31 228573_at 0.0001917 −2.5 ANTXR2 Anthrax toxin receptor 2 4q21.21 228577_x_at 0.0003076 2.8 ODF2L outer dense fiber of sperm tails 1p22.3 2-like (ODF2L), transcript variant 2, mRNA. 228579_at 7.00E−07 5.2 KCNQ3 Potassium voltage-gated 8q24 channel, KQT-like subfamily, member 3 228785_at 0.0006036 2.2 ZNF281 Zinc finger protein 281 1q32.1 228805_at 0.0003526 −3 FLJ44216 FLJ44216 protein (FLJ44216), 5q35.2 mRNA. 228841_at 0.0004789 −2 CDNA FLJ32429 fis, clone 5 SKMUS2001014 228850_s_at 0.0005294 2.8 SLIT2 Slit homolog 2 (Drosophila) 4p15.2 228885_at 1.82E−05 −4 MAMDC2 MAM domain containing 2 9q21.11 (MAMDC2), mRNA. 228905_at 0.0001087 −2.4 Transcribed locus, moderately 8 similar to XP_517655.1 PREDICTED: similar to KIAA0825 protein [Pan troglodytes] 228961_at 0.0004391 −2.1 FLJ35954 Hypothetical protein FLJ35954 5q11.2 229085_at 0.0003123 2.5 LRRC3B leucine rich repeat containing 3p24 3B (LRRC3B), mRNA. 229114_at 0.0002683 −2 GAB1 GRB2-associated binding 4q31.21 protein 1 229119_s_at 0.0001491 −2.2 TTC19 Hypothetical protein 17p12 LOC125150 229129_at 0.0006968 −2.2 HNRPD Heterogeneous nuclear 4q21.1-q21.2 ribonucleoprotein D (AU-rich element RNA binding protein 1, 37 kDa) 229130_at 0.0002067 −3 LOC285535 Hypothetical protein 4p16.1 LOC285535 229145_at 4.45E−05 −4.2 C10orf104 chromosome 10 open reading 10q22.1 frame 104 (C10orf104), mRNA. 229160_at 0.0003552 −6.5 MUM1L1 melanoma associated antigen Xq22.3 (mutated) 1-like 1 (MUM1L1), mRNA. 229200_at 0.000156 2.3 Hypothetical LOC400813 1q44 229204_at 0.0003007 2.2 HP1-BP74 Heterochromatin protein 1, 1p36.12 binding protein 3 229218_at 0.0003816 3.3 COL1A2 Collagen, type I, alpha 2 7q22.1 229221_at 0.0006672 4.1 CD44 CD44 antigen (homing function 11p13 and Indian blood group system) 229287_at 0.0007653 −2.8 Full-length cDNA clone 14 CS0DK010YA20 of HeLa cells Cot 25-normalized of Homo sapiens (human) 229299_at 0.0001103 −2.2 FLJ30596 hypothetical protein FLJ30596 5p13.2 (FLJ30596), mRNA. 229308_at 2.94E−05 −5.4 Transcribed locus 18 229319_at 0.0001521 −2.4 Homo sapiens, clone 6 IMAGE: 4105966, mRNA 229331_at 0.0007515 2.3 SPATA18 spermatogenesis associated 18 4q11 homolog (rat) (SPATA18), mRNA. 229339_at 0.0002425 −5 MYOCD Myocardin 17p11.2 229354_at 0.000578 3.3 PDCD6 Aryl-hydrocarbon receptor 5pter-p15.2 repressor 229431_at 0.000216 −2.1 RFXAP regulatory factor X-associated 13q14 protein (RFXAP), mRNA. 229483_at 0.0002012 2.5 UBE2H Ubiquitin-conjugating enzyme 7q32 E2H (UBC8 homolog, yeast) 229515_at 0.0002226 −2.2 PAWR PRKC, apoptosis, WT1 12q21 regulator 229520_s_at 0.0001174 2.3 C14orf118 Chromosome 14 open reading 14q22.1-q24.3 frame 118 229531_at 0.0007976 −2.2 Mitochondrial carrier triple Xq22.2 repeat 6 229553_at 0.0008476 2 PGM2L1 phosphoglucomutase 2-like 1 11q13.4 (PGM2L1), mRNA. 229580_at 0.0008828 −6.5 Transcribed locus 3 229638_at 0.0008539 2.9 IRX3 iroquois homeobox protein 3 16q12.2 (IRX3), mRNA. 229642_at 0.0002914 4.2 ARHGEF7 Rho guanine nucleotide 13q34 exchange factor (GEF) 7 (ARHGEF7), transcript variant 2, mRNA. 229665_at 0.0001871 2.2 CSTF3 Hypothetical protein 11p13 LOC283267 229711_s_at 0.0003052 2.1 CDNA FLJ37519 fis, clone 12 BRCAN2004699 229748_x_at 0.0001962 2.7 LOC285458 Hypothetical protein 4 LOC285458 229795_at 0.0002666 3.4 Transcribed locus 12 229801_at 0.0001036 3.4 C10orf47 chromosome 10 open reading 10p14 frame 47 (C10orf47), mRNA. 229830_at 0.0004695 3.9 PDGFA Platelet-derived growth factor 7p22 alpha polypeptide 229844_at 0.0001747 −2.2 Transcribed locus 3 229891_x_at 1.34E−05 −2.9 KIAA1704 KIAA1704 13q13-q14 229969_at 0.0003327 −2.5 Transcribed locus, moderately 6 similar to XP_508230.1 PREDICTED: zinc finger protein 195 [Pan troglodytes] 229994_at 0.0002738 −3 MRNA; cDNA 1 DKFZp686J23256 (from clone DKFZp686J23256) 230000_at 0.0004792 2.7 C17orf27 Chromosome 17 open reading 17q25.3 frame 27 230030_at 0.0003377 −5.2 HS6ST2 heparan sulfate 6-O- Xq26.2 sulfotransferase 2 (HS6ST2), mRNA. 230068_s_at 8.34E−05 −3.2 PEG3 paternally expressed 3 (PEG3), 19q13.4 mRNA. 230077_at 0.0001004 3.9 TFRC Transferrin receptor (p90, 3q29 CD71) 230081_at 5.00E−07 −6.1 PLCXD3 phosphatidylinositol-specific 5p13.1 phospholipase C, X domain containing 3 (PLCXD3), mRNA. 230130_at 9.27E−05 3 SLIT2 Slit homolog 2 (Drosophila) 4p15.2 230141_at 0.0002042 −2 ARID4A AT rich interactive domain 4A 14q23.1 (RBP1-like) 230174_at 0.0008233 −2.1 LYPLAL1 Lysophospholipase-like 1 1q41 230178_s_at 9.98E−05 −2.4 STATIP1 Signal transducer and activator 18q12.2 of transcription 3 interacting protein 1 230270_at 7.57E−05 2.9 ESTs 230333_at 0.0008148 2.5 SAT Spermidine/spermine N1- Xp22.1 acetyltransferase 230336_at 0.0008645 2.7 Transcribed locus 4 230369_at 0.0005567 −2.1 GPR161 G protein-coupled receptor 161 1q24.2 230387_at 0.0001569 3.1 ATP2C1 ATPase, Ca++ transporting, type 3q22.1 2C, member 1 230440_at 2.81E−05 3.3 ZNF469 PREDICTED: zinc finger 16 protein 469 (ZNF469), mRNA. 230561_s_at 0.0001454 −2.9 FLJ23861 hypothetical protein FLJ23861 2q34 (FLJ23861), mRNA. 230574_at 0.0008056 2.9 Hypothetical LOC388480 18q21.33 230746_s_at 1.50E−06 13.3 STC1 stanniocalcin 1 (STC1), mRNA. 8p21-p11.2 230758_at 0.00064 −2.6 Transcribed locus X 230793_at 7.34E−05 −3.1 LRRC16 leucine rich repeat containing 16 6p22.2 (LRRC16), mRNA. 230850_at 0.0001807 3 FMNL3 Formin-like 3 12q13.12 230885_at 0.0001271 2.2 SPG7 Spastic paraplegia 7, paraplegin 16q24.3 (pure and complicated autosomal recessive) 230958_s_at 4.15E−05 −2.1 MRNA; cDNA 1 DKFZp686J23256 (from clone DKFZp686J23256) 231130_at 0.0009273 −2 FKBP7 FK506 binding protein 7 2q31.2 231183_s_at 0.000129 4.3 JAG1 jagged 1 (Alagille syndrome) 20p12.1-p11.23 (JAG1), mRNA. 231202_at 0.0002962 3.1 FLJ38508 Aldehyde dehydrogenase 1 12q23.3 family, member L2 231411_at 0.0001224 3.2 LHFP lipoma HMGIC fusion partner 13q12 (LHFP), mRNA. 231597_x_at 0.0001876 15.9 ESTs, Weakly similar to T47135 hypothetical protein DKFZp761L0812.1 [H. sapiens] 231806_s_at 0.0009603 2.1 STK36 serine/threonine kinase 36 2q35 (fused homolog, Drosophila) (STK36), mRNA. 231825_x_at 8.13E−05 3.6 ATF7IP Activating transcription factor 7 12p13.1 interacting protein 231882_at 0.0002463 2.7 CDNA FLJ10674 fis, clone 22 NT2RP2006436 231886_at 0.0003613 3 Similar to hypothetical protein 3q29 LOC284701 232034_at 0.0008165 3.9 LOC203274 Hypothetical protein 9q21.11 LOC203274 232145_at 0.0002539 2.1 LOC388969 hypothetical LOC388969 2p11.2 (LOC388969), mRNA. 232150_at 2.29E−05 3.1 C20orf18 Chromosome 20 open reading 20p13 frame 18 232169_x_at 0.0002893 3.1 NDUFS8 NADH dehydrogenase 11q13 (ubiquinone) Fe—S protein 8, 23 kDa (NADH-coenzyme Q reductase) 232174_at 7.00E−06 4.1 EXT1 Exostoses (multiple) 1 8q24.11-q24.13 232180_at 8.56E−05 3.2 UGP2 UDP-glucose 2p14-p13 pyrophosphorylase 2 232215_x_at 0.0001855 3.4 FLJ11029 Hypothetical protein FLJ11029 17q23.2 232254_at 8.75E−05 2.5 FBXO25 F-box protein 25 8p23.3 232266_x_at 0.0001426 3.9 CDC2L5 Cell division cycle 2-like 5 7p13 (cholinesterase-related cell division controller) 232304_at 2.60E−06 4 PELI1 Pellino homolog 1 (Drosophila) 2p13.3 232347_x_at 0.0001636 2.6 CBR4 Carbonic reductase 4 4q32.3 232406_at 0.0001583 2.9 JAG1 Jagged 1 (Alagille syndrome) 20p12.1-p11.23 232458_at 1.67E−05 4.1 COL3A1 Collagen, type III, alpha 1 2q31 (Ehlers-Danlos syndrome type IV, autosomal dominant) 232516_x_at 7.53E−05 3.3 YAP YY1 associated protein 1 1q22 232530_at 0.0006114 2.8 PLD1 Phospholipase D1, 3q26 phophatidylcholine-specific 232538_at 0.0008933 2.4 CDNA: FLJ23573 fis, clone 16 LNG12520 232541_at 0.0007593 3.5 EGFR Epidermal growth factor 7p12 receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) 232617_at 8.18E−05 3.2 CTSS cathepsin S (CTSS), mRNA. 1q21 232653_at 0.000473 3.5 Homo sapiens cDNA FLJ14044 fis, clone HEMBA1006124 232702_at 0.0006941 3 RABGAP1L RAB GTPase activating protein 1q24 1-like 232797_at 0.0008213 2.3 ITGAV Integrin, alpha V (vitronectin 2q31-q32 receptor, alpha polypeptide, antigen CD51) 232814_x_at 0.0005021 2.8 C14orf153 Chromosome 14 open reading 14q32.32-q32.33 frame 153 232889_at 0.0003899 2.6 CDNA clone IMAGE: 5576908 5 232952_at 0.0001405 2.7 DDEF1 HSPC054 protein 8q24.1-q24.2 233041_x_at 0.0004112 3 BTBD9 BTB (POZ) domain containing 9 6p21 233180_at 1.17E−05 2.8 RNF152 Ring finger protein 152 18q21.33 233274_at 3.00E−07 3.6 NCK1 NCK adaptor protein 1 3q21 233319_x_at 0.0001543 3.1 PHACTR4 Phosphatase and actin regulator 4 1p35.3 233330_s_at 4.59E−05 5.6 Similar to Ribosome biogenesis 9q13 protein BMS1 homolog 233406_at 0.0002846 2.9 KIAA0256 KIAA0256 gene product 15q21.1 233496_s_at 0.0003586 −2 CFL2 Cofilin 2 (muscle) 14q12 233702_x_at 0.0007629 3.1 CDNA: FLJ20946 fis, clone 7 ADSE01819 233849_s_at 0.0005935 −2.3 ARHGAP5 Rho GTPase activating protein 5 14q12 (ARHGAP5), transcript variant 2, mRNA. 233912_x_at 1.73E−05 4.4 ELMOD2 ELMO domain containing 2 4q31.21 234192_s_at 0.0001567 −3.1 GKAP1 G kinase anchoring protein 1 9q21.32 (GKAP1), mRNA. 234339_s_at 6.34E−05 −2.4 GLTSCR2 glioma tumor suppressor 19q13.3 candidate region gene 2 (GLTSCR2), mRNA. 234464_s_at 4.21E−05 3 EME1 essential meiotic endonuclease 1 17q21.33 homolog 1 (S. pombe) (EME1), mRNA. 234512_x_at 2.40E−06 −3.1 LOC442159 PREDICTED: similar to Rpl7a 6 protein (LOC442159), mRNA. 234562_x_at 1.80E−06 8.6 CKLFSF8 Chemokine-like factor super 3p23 family 8 234578_at 7.26E−05 4.9 MRNA; cDNA 1 DKFZp434E1812 (from clone DKFZp434E1812) 234675_x_at 6.52E−05 4.3 CDNA: FLJ23566 fis, clone 14 LNG10880 234723_x_at 1.50E−06 9.4 CDNA: FLJ21228 fis, clone 7 COL00739 234753_x_at 0.0002577 5.7 234762_x_at 8.75E−05 4.1 NLN Neurolysin (metallopeptidase 5q12.3 M3 family) 234788_x_at 0.0001541 3.3 FLJ13611 Hypothetical protein FLJ13611 5q12.3 234873_x_at 0.000607 −2 234981_x_at 9.85E−05 4.4 LOC134147 Similar to mouse 5p15.2 2310016A09Rik gene 234985_at 9.30E−06 2.9 LOC143458 Hypothetical protein 11p13 LOC143458 234998_at 0.0009467 −2.7 CDNA clone IMAGE: 5313062 15 235005_at 0.0003344 −2.3 MGC4562 Hypothetical protein MGC4562 15q22.31 235061_at 0.0002578 −2.9 PPM1K protein phosphatase 1K (PP2C 4q22.1 domain containing) (PPM1K), mRNA. 235072_s_at 6.66E−05 −3 Transcribed locus 6 235122_at 5.42E−05 3.1 CDNA clone IMAGE: 6254031 1 235151_at 0.0004926 −2.1 LOC283357 Hypothetical protein 12p13.33 LOC283357 235204_at 1.87E−05 3.1 ENTPD7 Ectonucleoside triphosphate 10 diphosphohydrolase 7 235205_at 0.0001252 3.5 LOC346887 PREDICTED: similar to solute 8 carrier family 16 (monocarboxylic acid transporters), member 14 (LOC346887), mRNA. 235278_at 0.0002619 −3.6 C20orf133 chromosome 20 open reading 20p12.1 frame 133 (C20orf133), transcript variant 2, mRNA. 235309_at p < 1e−07 −4.9 CDNA clone IMAGE: 4140029 16 235327_x_at 0.0002751 2.9 UBXD4 UBX domain containing 4 2p23.3 (UBXD4), mRNA. 235343_at 3.96E−05 4.2 FLJ12505 Hypothetical protein FLJ12505 1q32.3 235374_at 3.04E−05 2.7 MDH1 Malate dehydrogenase 1, NAD 2p13.3 (soluble) 235412_at 0.0002124 3.2 ARHGEF7 Rho guanine nucleotide 13q34 exchange factor (GEF) 7 235433_at 0.0003304 −2.2 SATL1 Spermidine/spermine N1-acetyl Xq21.1 transferase-like 1 235556_at 0.0001833 −2 Transcribed locus, weakly 5 similar to NP_703324.1 glutamic acid-rich protein (garp) [Plasmodium falciparum 3D7] 235601_at 0.0003888 2.7 ESTs 235612_at 2.90E−05 −3.1 Transcribed locus, moderately 1 similar to NP_858931.1 NFS1 nitrogen fixation 1 isoform b precursor; cysteine desulfurase; nitrogen-fixing bacteria S-like protein; nitrogen fixation 1 (S. cerevisiae, homolog) [Homo sapiens] 235628_x_at 0.0004866 2.4 Hypothetical protein 5q23.2 LOC133926 235693_at 0.0003764 2.9 Transcribed locus 5 235725_at 0.0004132 −2.2 Transcribed locus 14 235927_at 6.41E−05 2.4 XPO1 Exportin 1 (CRM1 homolog, 2p16 yeast) 235944_at 0.0004031 3.3 HMCN1 hemicentin 1 (HMCN1), 1q25.3-q31.1 mRNA. 236249_at 1.54E−05 2.7 IKIP IKK interacting protein (IKIP), 12q23.1 transcript variant 1, mRNA. 236251_at 8.16E−05 2.7 ITGAV Integrin, alpha V (vitronectin 2q31-q32 receptor, alpha polypeptide, antigen CD51) 236678_at 0.0005987 2.8 JAG1 Jagged 1 (Alagille syndrome) 20p12.1-p11.23 236715_x_at 0.0002206 2.5 UACA uveal autoantigen with coiled- 15q22-q24 coil domains and ankyrin repeats (UACA), transcript variant 1, mRNA. 236829_at 6.57E−05 2.9 TMF1 TATA element modulatory 3p21-p12 factor 1 236883_at 0.0003076 2.6 ESTs 236936_at 0.0007927 −2.4 Transcribed locus 8 236966_at 0.0004757 2.6 TXNDC6 thioredoxin domain containing 6 3q22.3 (TXNDC6), mRNA. 236974_at 0.0003599 2.5 CCNI Cyclin I 4q21.1 237206_at 0.0003483 −5.9 MYOCD Myocardin 17p11.2 237333_at 0.0008796 −2 SYNCOILIN Syncoilin, intermediate filament 1 1p34.3-p33 237475_x_at 0.0001562 4.3 SEPP1 Selenoprotein P, plasma, 1 5q31 237494_at 2.03E−05 3.2 Transcribed locus 15 237868_x_at 0.000358 3 ESTs, Weakly similar to ALUF_HUMAN !!!! ALU CLASS F WARNING ENTRY !!! [H. sapiens] 238026_at 0.0007905 −2 RPL35A Ribosomal protein L35a 3q29-qter 238142_at 0.000678 2.4 LOC253982 Hypothetical protein 16p11.2 LOC253982 238183_at 0.0001644 3.7 ESTs 238273_at 0.0007281 2 Full-length cDNA clone 7 CS0DB005YG10 of Neuroblastoma Cot 10- normalized of Homo sapiens (human) 238327_at 6.09E−05 2.6 Similar to MGC52679 protein 22q13.33 238478_at 0.000183 −3.7 BNC2 Basonuclin 2 9p22.3-p22.2 238584_at 0.0002196 3.3 IQCA IQ motif containing with AAA 2q37.2-q37.3 domain 238613_at 8.97E−05 −2.7 ZAK sterile alpha motif and leucine 2q24.2 zipper containing kinase AZK (ZAK), transcript variant 2, mRNA. 238642_at 0.0003128 3 LOC338692 Ankyrin repeat domain 13 11q13.2 family, member D 238673_at 6.02E−05 4.7 Transcribed locus 8 238714_at 0.0001825 2.5 RAB12, member RAS oncogene 18p11.22 family 238719_at 0.0004981 −2.5 PPP2CA Protein phosphatase 2 (formerly 5q31.1 2A), catalytic subunit, alpha isoform 238852_at 0.0003011 2.3 ESTs 238878_at 0.0006945 −6.2 ARX Aristaless related homeobox Xp22.1-p21.3 239227_at 9.04E−05 3 EXT1 Exostoses (multiple) 1 8q24.11-q24.13 239246_at 0.0002103 3 FARP1 FERM, RhoGEF (ARHGEF) 13q32.2 and pleckstrin domain protein 1 (chondrocyte-derived) 239258_at 0.0009901 3.1 RHOQ Ras homolog gene family, 2p21 member Q 239262_at 3.72E−05 −3.8 CDNA FLJ26242 fis, clone 11 DMC00770 239264_at 0.0003642 2.2 SEC8L1 SEC8-like 1 (S. cerevisiae) 7q31 239367_at 0.0001649 3.1 BDNF brain-derived neurotrophic 11p13 factor (BDNF), transcript variant 6, mRNA. 239516_at 0.0001834 2.7 LYPLAL1 Lysophospholipase-like 1 1q41 239540_at 0.0009106 2.6 GTF3C1 General transcription factor IIIC, 16p12 polypeptide 1, alpha 220 kDa 239748_x_at 0.0003286 3.7 OCIA ovarian carcinoma 4p11 immunoreactive antigen 239806_at 0.000252 4.4 Transcribed locus 2 239848_at 0.0005816 −2.7 GA17 Dendritic cell protein 11p13 240216_at 0.0001639 2.6 ZBTB20 Zinc finger and BTB domain 3q13.2 containing 20 240421_x_at 0.0001971 3.7 CDNA clone IMAGE: 5268630 4 240655_at 3.01E−05 4.3 ALCAM Activated leukocyte cell 3q13.1 adhesion molecule 240795_at 0.0001514 2.3 CDNA clone IMAGE: 5288566 5 241223_x_at 0.0002281 3.2 ESTs, Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 241268_x_at 0.0008446 3.5 SAMHD1 SAM domain and HD domain 1 20pter-q12 241303_x_at 0.0007123 2.9 ESTs 241387_at 0.0008125 2.7 PTK2 PTK2 protein tyrosine kinase 2 8q24-qter 241421_at 0.0005012 2.6 Transcribed locus 1 241435_at 1.52E−05 4.4 ETS1 V-ets erythroblastosis virus E26 11q23.3 oncogene homolog 1 (avian) 241617_x_at 0.000334 2.6 ESTs, Weakly similar to 810024C cytochrome oxidase I [H. sapiens] 241627_x_at 0.0005548 2.9 FLJ10357 Hypothetical protein FLJ10357 14q11.2 241632_x_at 3.70E−06 3.3 ESTs 241686_x_at 3.28E−05 4.4 ESTs, Weakly similar to hypothetical protein FLJ20378 [Homo sapiens] [H. sapiens] 241718_x_at 7.37E−05 3.4 ESTs 241727_x_at 0.0003166 2.3 DHFRL1 dihydrofolate reductase-like 1 3q11.2 (DHFRL1), mRNA. 241769_at 0.0004802 2.5 ITGAV Integrin, alpha V (vitronectin 2q31-q32 receptor, alpha polypeptide, antigen CD51) 241809_at 0.0001618 2.5 LOC284465 Hypothetical protein 1p13.2 LOC284465 242029_at 9.60E−06 3.7 FNDC3B Fibronectin type III domain 3q26.31 containing 3B 242051_at 6.20E−06 −3.7 Transcribed locus X 242100_at 2.40E−06 4.8 CSS3 chondroitin sulfate synthase 3 5q23.3 (CSS3), mRNA. 242171_at 0.0007535 3.1 ESTs, Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 242233_at 7.63E−05 2.4 KIAA1219 KIAA1219 protein 20q11.23 242240_at 0.0001413 3 PTK2 PTK2 protein tyrosine kinase 2 8q24-qter 242329_at 8.94E−05 3.1 LOC401317 PREDICTED: hypothetical 7 LOC401317 (LOC401317), mRNA. 242363_at 9.05E−05 −2.7 DNCI2 Dynein, cytoplasmic, 2q31.1 intermediate polypeptide 2 242364_x_at 0.0001237 3.1 EVER1 Epidermodysplasia 17q25.3 verruciformis 1 242369_x_at 7.20E−06 4.1 NCOA2 Nuclear receptor coactivator 2 8q13.3 242398_x_at 3.00E−06 6.1 MEP50 WD repeat domain 77 1p13.2 242405_at 4.08E−05 2 MAML2 Mastermind-like 2 (Drosophila) 11q21 242488_at 2.11E−05 −4.7 CDNA FLJ38396 fis, clone 1 FEBRA2007957 242500_at 0.0007278 2.6 Transcribed locus 6 242546_at 2.70E−06 5.4 LOC440156 14q11.1 242578_x_at 0.0002453 4 SLC22A3 Solute carrier family 22 6q26-q27 (extraneuronal monoamine transporter), member 3 242862_x_at 6.29E−05 5.2 ESTs 242999_at 0.0007732 2.3 ARHGEF7 Rho guanine nucleotide 13q34 exchange factor (GEF) 7 (ARHGEF7), transcript variant 2, mRNA. 243_g_at 9.74E−05 2.1 MAP4 microtubule-associated protein 4 3p21 (MAP4), transcript variant 2, mRNA. 243006_at 1.10E−06 4.7 FYN FYN oncogene related to SRC, 6q21 FGR, YES 243147_x_at 7.12E−05 5.7 ESTs, Weakly similar to RMS1_HUMAN REGULATOR OF MITOTIC SPINDLE ASSEMBLY 1 [H. sapiens] 243249_at 7.21E−05 2.4 ESTs, Weakly similar to hypothetical protein FLJ20378 [Homo sapiens] [H. sapiens] 243305_at 0.0003329 2.9 KIAA1340 Kelch domain containing 5 12p11.22 243442_x_at 0.0001001 3.7 ESTs, Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 243846_x_at 0.0007887 3 FLJ32810 Hypothetical protein FLJ32810 11q22.1 243915_at 0.0001482 2.9 ESTs, Weakly similar to 2109260A B cell growth factor [H. sapiens] 244007_at 0.000373 −2 Transcribed locus 9 244022_at 0.0007683 2 FNDC3B Fibronectin type III domain 3q26.31 containing 3B 244050_at 0.0001908 −2.6 LOC401494 similar to RIKEN 4933428I03 9p21.3 (LOC401494), mRNA. 244188_at 0.0004372 3.1 FLJ21924 Hypothetical protein FLJ21924 11p13 244193_at 0.0003257 2.1 FLJ13236 Hypothetical protein FLJ13236 12q13.12 244197_x_at 2.30E−05 3.3 CNOT2 CCR4-NOT transcription 12q15 complex, subunit 2 244457_at 8.66E−05 3.1 ITPR2 Inositol 1,4,5-triphosphate 12p11 receptor, type 2 244503_at 0.0004105 2.5 ESTs 244633_at 0.000111 2.5 PIAS2 Protein inhibitor of activated 18q21.1 STAT, 2 244648_at 0.0003403 3.5 FLJ10996 Hypothetical protein FLJ10996 2q14.1 244745_at 0.0006739 −2.7 RERG RAS-like, estrogen-regulated, 12p12.3 growth inhibitor (RERG), mRNA. 31874_at 8.21E−05 2.9 GAS2L1 Growth arrest-specific 2 like 1 22q12.2 33323_r_at 0.0001426 5.1 SFN Stratifin 1p36.11 38069_at 0.0003197 2 CLCN7 chloride channel 7 (CLCN7), 16p13 mRNA. 38671_at 0.0003864 2.4 PLXND1 plexin D1 (PLXND1), mRNA. 3q21.3 39549_at 0.0008832 2.5 NPAS2 neuronal PAS domain protein 2 2q11.2 (NPAS2), mRNA. 39891_at 0.0005541 2.2 DKFZp547K1113 Hypothetical protein 15q26.1 DKFZp547K1113 40524_at 3.70E−05 2.8 PTPN21 protein tyrosine phosphatase, 14q31.3 non-receptor type 21 (PTPN21), mRNA. 41856_at 0.0008627 2.3 UNC5B Unc-5 homolog B (C. elegans) 10q22.1 44783_s_at 6.85E−05 3 HEY1 hairy/enhancer-of-split related 8q21 with YRPW motif 1 (HEY1), mRNA. 46665_at 5.11E−05 2.4 SEMA4C sema domain, immunoglobulin 2q11.2 domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C (SEMA4C), mRNA. 47550_at 3.40E−05 4.4 LZTS1 leucine zipper, putative tumor 8p22 suppressor 1 (LZTS1), mRNA. 50376_at 0.000154 2.1 ZNF444 zinc finger protein 444 19q13.43 (ZNF444), mRNA. 52255_s_at 1.15E−05 6.1 COL5A3 collagen, type V, alpha 3 19p13.2 (COL5A3), mRNA. 55583_at 0.0001374 3.2 DOCK6 dedicator of cytokinesis 6 19p13.2 (DOCK6), mRNA. 57539_at 0.0006736 2.1 ZGPAT zinc finger, CCCH-type with G 20q13.3 patch domain (ZGPAT), transcript variant 3, mRNA. 57703_at 0.0001957 2.4 SENP5 SUMO1/sentrin specific 3q29 peptidase 5 (SENP5), mRNA. 57739_at 0.0004289 2.2 DND1 Dead end homolog 1 (zebrafish) 5q31.3 59433_at 5.44E−05 2.2 Transcribed locus X 61734_at 3.36E−05 2.7 RCN3 Reticulocalbin 3, EF-hand 19q13.33 calcium binding domain

As indicated in Table 1, 652 genes were up-regulated ≧2-fold in ovarian cancer endothelium samples. Of the 652 genes that were up-regulated ≧2-fold, 35 genes were elevated at least 6-fold in tumor endothelium (Table 2), with 7 being elevated more than 10-fold and 2 being elevated more than 28-fold.

TABLE 2 Genes up-regulated by ≧6-fold in the tumor associated endothelium. Entrez Fold chromosomal Gene ID Gene Description difference location Function 25975 EGFL6 EGF-like-domain, 36.8 Xp22 May regulate cell cycle and Multiple 6 oncogenesis 7130 TNFAIP6 Tumor necrosis factor, 29.1 2q23.3 Anti-inflammatory and Alpha-induced protein 6 chondroprotective effect 7291 TWIST1 Basic helix-loop-helix 19.0 7p21.2 Inhibits chondrogenesis (bHLH) transcription factor 6781 STC1 Stanniocalcin 1 13.3 8p21-p11.2 Regulates calcium/ phosphate homeostasis, and cell metabolism 84525 HOP Homeodomain-only 13.1 4q11-q12 Transcriptional repressor. Protein, transcript Modulates serum response variant 2 factor-dependent cardiac- specific gene expression and cardiac development 1462 CSPG2 Chondroitin sulfate 10.4 5q14.3 Extracellular matrix proteoglycan 2 component of the vitreous gel. (versican) Anti-cell adhesive. 57125 PLXDC1 Plexin domain 10.2 17q21.1 Unknown containing 1 6696 SPP1 Secreted 9.5 4q21-q25 Expressed during phosphoprotein 1 embryogenesis, wound (osteopontin, bone healing, and tumorigenesis. sialoproteinI, Regulates the assembly of Early T-lymphocyte heterotypic fibers composed of activation1) both type 1 and type V collagen. 4318 MMP9 Matrix metallopeptidase 9 9.4 20q11.2-q13.1 Breakdown of extracellular (gelatinase B, 92 kDa matrix. Plays a role in type IV collagenase) angiogenesis and tumor invasion 3937 LCP2/SLP76 Lymphocyte cytosolic 8.7 5q33.1-qter Promotes T-cell protein 2 (SH2 domain development and containing Leukocyte activation protein of 76 kDa) 152189 CKLFSF8 Chemokine-like factor 8.6 3p23 Regulates EGF-induced Superfamily 8 signaling. Regulates cell proliferation 5366 PMAIP1 Phorbol-12-myristate- 8.5 18q21.32 Unknown 13-acetate-induced protein 1 24147 FJX1 Four jointed box 1 7.7 11p13 In drosophila, a downstream (drosophila) target of the Notch signaling pathway, regulates cell growth and differentiation. Not known in human 8038 ADAM12 ADAM metallo- 7.6 10q26.3 Critical for tumor peptidase domain 12 development. Involved in cell- (meltrin alpha) cell and cell-matrix interactions. 9636 GIP2 Interferon, alpha- 6.9 1p36.33 Unclear, may be related to inducible protein (clone regulation of cell proliferation IFI-15K) and differentiation 25878 MXRA5 Matrix-remodeling 6.9 Xp22.33 Matrix remodeling associated 5 1123 CNH1 Chimerin 6.9 2q31-q32.1 Rho GTPase activating protein (chimaerin) 1 3310 HSPA6 Heat shock 70 KDa 6.8 1q23 Involved in protein protein 6 (HSP70B) conformational interactions 11211 FZD10 Frizzled homolog 10 6.7 12q24.33 Receptor for the wingless (Drosophila) Type MMTV integration site family. 10631 POSTN Periostin, osteoblast 6.7 13q13.3 Promotes integrin-dependent specific factor cell adhesion and motility, involved in extracellular matrix deposition 85477 SCIN Scinderin 6.6 7p21.3 Ca²⁺ dependent actin filament severing protein, regulates cortical actin network dynamics 27242 TNFRSF21 Tumor necrosis factor 6.6 6p21.1-12.2 Unclear; maybe related to Receptor superfamily, activation of NF-kappaB and Member 21 MAPK8/JNK, induces cell apoptosis, involved in inflammation and immune regulation. 25891 DKFZP586- Regeneration associated 6.2 11p13 Unknown H2123 muscle protease, transcript variant 2 4582 MUC1 Mucin 1, 6.2 1q21 Regulates cell aggregation, transmembrane, adhesion transcript variant 4 79084 MEP50 WD repeat domain 77, 6.1 1p13.2 Involved in the methylation WDR77 and assembly of spliceosomal snRNAs Sm proteins 50509 COL5A3 Collagen, type V, alpha 3 6.1 19p13.2 Extracellular protein, associated with formation of fibrils, and some connective tissue pathology such as inflammation, cancer and atherosclerosis 6205 RPS11 Ribosomal protein S11 6.1 19q13.3 Involved in the recognition of termination codons. 55803 CENTA2 Centaurin, alpha 2 6.1 17q11.2 A phosphatidylinositide- binding protein present in the dense membrane fractions of cell extracts 2295 FOXF2 Forkhead box F2 6.0 6p25.3 Regulates cell proliferation and survival, associated with BMP and Wnt signaling

TABLE 3 Genes down-regulated in tumor associated endothelium. Entrez Chromosomal Gene ID Gene Description Fold difference location Function 5350 PLN Phospholamban 0.108 6q22.1 Inhibits sarcoplasmic reticulum Ca(2+)- ATPase activity 6401 SELE Selectin E, 0.112 1q22-q25 Cell surface lycoprotein. endothelial Inhibits cell adhesion. Adhesion molecule 1 Early marker of inflammation 9687 GREB1 GREB1 protein, 0.116 2p25.1 Transcription factor, transcript variant a inhibits cell proliferation 4969 OGN Osteoglycin 0.147 9q22 Regulates collagen osteoinductive fibrillogenesis Factor, mimecan), transcript variant 3 25890 AB13BP ABI gene family, 0.152 3q12 May play a role in cell member 3 (NESH) motility by regulating binding protein NESH function 90161 HS6ST2 Heparn sulfate 6- 0.153 Xq26.2 Plays a role in growth O-sulfotransferase 2 factor signaling, cell adhesion, and enzymatic catalysis. Maybe involved in vascularization by mediating FGF signaling 139221 MUM1L1 Melanoma associated 0.155 Xq22.3 Encodes tumor specific antigen (mutated) 1- antigens like 1 4129 MAOB Monoamine oxidase B 0.156 Xp11.23 Regulates neurotransmitters in central nervous system 9452 ITM2A Integral membrane 0.156 Xq13.3-Xq21.2 Transmembrane protein. protein 2A Marker of early stage of endochondral ossification 170302 ARX Aristaless related 0.162 Xp22.1-p21.3 Organ development. homeobox Bifunctional transcription factor 10659 CUGBP2 CUG triplet repeat, 0.163 10p13 Binds and stabilizes RNA binding Protein COX2 mRNA, inhibits 2, transcript variant 2 its translation 5577 PRKAR2B Protein kinase, 0.163 7q22 Encodes a regulatory cAMP-dependent subunit RII beta of regulatory, type II, human cAMP-dependent beta protein kinase A 345557 LCXD3 Phosphatidylinositol- 0.165 5p13.1 Quantitatively specific solubilizes phospholipase C, X AChE from purified domain containing 3 synaptic plasma membranes and intact synaptosomes of Torpedo ocellata electric organ

Multiple genes encoding proteins involved in extracellular matrix function, such as collagens, TNFAIP6, ADAMTS4, MMP9, MMP11, had increased expression in tumor vasculature compared with normal ovarian vasculature. The α_(v) integrin (vitronectin receptor) was elevated 2.5-fold in tumor endothelium. Several transcription factors were upregulated in the ovarian cancer vasculature. For example, HEYL was increased 3-fold. In addition, several transcription factors were identified including E2F transcription factor 3 (E2F3; plays a role in cell proliferation) (Black, Proc Natl Acad Sci U.S.A. 102: 15948-15953, 2005); runt-related transcription factor 1 (RUNX1; plays a role in angiogenesis) (Iwatsuki et al., Oncogene 24: 1129-1137, 2005), signal transducer and activator of transcription 2 (STAT2; role in cellular proliferation) (Gomez and Reich, J. Immunol. 170: 5373-5381, 2003), the SNAIL-related zinc-finger transcription factor, SLUG (SNAI2) (Perez-Mancera et al., Oncogene 24: 3073-3082, 2005), and Twist1 (Mironchik et al. Cancer Res. 65: 10801-10809, 2005). These genes were elevated 2-18 fold in the ovarian cancer vasculature relative to normal ovarian endothelial cells.

Additional genes were identified as being overexpressed in ovarian tumor endothelial cells that had previously been reported to be overexpressed in tumor cells. For example, epidermal growth factor receptor (EGFR) expression was increased by 3.5-fold in the tumor endothelium. EGFR is known to be overexpressed in ovarian carcinomas and is predictive of poor outcome (Berchuck et al., Am. J. Obstet. Gynecol. 164: 669-674, 1991). Similarly, non-receptor kinases such as focal adhesion kinase (FAK or PTK2; 3.1-fold increase) and Fyn (4.7 fold increase), which are play functional roles for tumor cells were detected. Genes that are overexpressed on both tumor cells and tumor-associated endothelial cells are targets for anti-vascular therapy due to the ability to target both the epithelial and stromal compartments.

In addition to the 652 genes that were identified as being up-regulated in ovarian tumor endothelial cells, 497 genes were down-regulated ≧2-fold in ovarian cancer endothelium samples (Table 1). FIG. 1 illustrates the fold changes observed in the relative expression levels between microarray data and real-time quantitative RT-PCR data from the pro-angiogenic gene signature provided in Table 1. Of the 497 genes that were down-regulated ≧2-fold, 17 genes were decreased at least 6-fold (as provide in Table 3). For example, monoamine oxidase B (MAOB), a gene responsible for detoxification and degradation of monoamines was decreased by 6.4-fold in the tumor endothelial cells (Grimsby et al., Nat. Genet. 17: 206-210, 1997). Decorin, a small multi-functional proteoglycan with anti-angiogenic properties, was decreased by 4.8-fold (Sulochana et al., J. Biol. Chem. 280: 27935-27948, 2005). Several other genes with potential anti-angiogenic or anti-proliferative roles such as Fibulin-5 (FBLN-5) and checkpoint suppressor 1 (CHES1) were down-regulated by 4.5-fold and 4.3-fold, respectively (Albig and Schiemann, DNA Cell Biol. 23: 367-379, 2004; and Scott and Plon, Gene 359: 119-126, 2005). These findings indicate that tumor endothelial cell and non-tumor endothelial cell isolates possess distinct expression profiles.

Example 4 Identification of Tumor Endothelial Markers

This example provides specific tumor endothelial cell markers.

Differentially regulated genes expressed in tumor-associated endothelium were identified by comparing tumor-associated endothelium versus normal endothelium with tumor-associated epithelial cells versus ovarian surface epithelium (OSE). The expression profile of microdissected papillary serous ovarian cancers using the same microarray methods has previously been reported (Bonome et al. Cancer Res. 65: 10602-10612, 2005). The current disclosed list of differentially expressed genes in tumor-associated endothelial cells was compared with the gene list identified for laser microdissected tumor-epithelial cells. A total of 534 differentially regulated genes were uniquely altered (up- or down-regulated) in the endothelial cells. The 28 genes with the greatest level of increase in ovarian tumor endothelial cells are listed in Table 4, of which 23 genes had a ≧6-fold increase in expression. A complete listing of the 534 differentially regulated genes is provided in Table 5. Further, FIG. 2 illustrates protein expression levels detected in ovarian endothelial cells following staining of samples with immunofluorescently-labeled PTK2, Fyn, MMP-9, β2-arrestin, Jagged1 and PLXDC1, respectively.

These findings identify tumor endothelial cell specific genes that can be used as biomarkers and potential targets for treatment of ovarian cancer.

TABLE 4 Genes specifically regulated in tumor-endothelium Entrez Fold Chromosomal Gene ID Gene Description difference location Function 25975 EGFL6 EGF-like-domain, multiple 6 36.848 Xp22 May regulate cell cycle (EGFL6) and oncogenesis 7130 TNFAIP6 Tumor necrosis factor, alpha- 29.062 2q23.3 Anti-inflammatory and induced protein 6 (TNFAIP6) chondroprotective effect 7291 TWIST1 Twist homolog 1 18.969 7p21.2 Inhibits chondrogenesis (acrocephalosyndactyly 3; Saethre-Chotzen syndrome) (Drosophila) (TWIST1) 6781 STC1 Stanniocalcin 1 (STC1) 13.326 8p21-p11.2 Regulates calcium/ phosphate homeostasis, and cell metabolism 84525 HOP Homeodomain-only protein 13.144 4q11-q12 Transcriptional (HOP), transcript variant 2 repressor. Modulates serum response factor-dependent cardiac-specific gene expression and cardiac development 1462 CSPG2 Chondroitin sulfate 10.355 5q14.3 Extracellular matrix proteoglycan 2 (versican) component of the (CSPG2) vitreous gel. Anti-cell adhesive. 57125 PLXDC1 Plexin domain containing 1 10.215 17q21.1 Unknown (PLXDC1) 4318 MMP9 Matrix metallopeptidase 9 9.389 20q11.2-q13.1 Breakdown of (gelatinase B, 92 kDa extracellular gelatinase, 92 kDa type IV matrix. Plays a role in collagenase) (MMP9) angiogenesis and tumor invasion 3937 LCP2 Lymphocyte cytosolic protein 8.744 5q33.1-qter Promotes T-cell 2 (SH2 domain containing development and leukocyte protein of 76 kDa) activation (LCP2) 5366 PMAIP1 Phorbol-12-myristate-13- 8.543 18q21.32 Unknown acetate-induced protein 1 (PMAIP1) 8038 ADAM12 ADAM metallopeptidase 7.605 10q26.3 Involved in cell-cell and domain 12 (meltrin alpha) cell-matrix interactions (ADAM12), transcript variant 1 25878 MXRA5 Matrix-remodeling associated 6.865 Xp22.33 Matrix remodeling 5 (MXRA5) 1123 CHN1 Chimerin (chimaerin) 1 6.857 2q31-q32.1 Rho GTPase activating (CHN1) protein 3310 HSPA6 Heat shock 70 kDa protein 6 6.76 1q23 Involved in protein conformational interactions 10631 POSTN Periostin, osteoblast specific 6.732 13q13.3 Promotes integrin- factor (POSTN) dependent cell adhesion and motility, involved in extracellular matrix deposition 11211 FZD10 Frizzled homolog 10 6.701 12q24.33 Receptor for the (Drosophila) (FZD10) wingless type MMTV integration site family 27242 TNFRSF21 Tumor necrosis factor 6.649 6p21.1-12.2 Activates NF-kappaB receptor superfamily, member and MAPK8/JNK, 21 (TNFRSF21) induces cell apoptosis, involved in inflammation and immune regulation. 25891 DKFZP586H2123 Regeneration associated 6.199 11p13 Unknown muscle protease, transcript variant 2 79084 MEP50 WD repeat domain 77 6.144 1p13.2 Involved in the methylation and assembly of spliceosomal snRNAs Sm proteins 50509 COL5A3 Collagen, type V, alpha 3 6.118 19p13.2 Extracellular protein, (COL5A3) associated with formation of fibrils, and some connective tissue pathology such as inflammation, cancer and atherosclerosis 6205 RPS11 Ribosomal protein S11 6.095 19q13.3 Involved in the (RPS11) recognition of termination codons 55803 CENTA2 Centaurin, alpha 2 (CENTA2) 6.09 17q11.2 A phosphatidylinositide- binding protein present in the dense membrane fractions of cell extracts 90161 HS6ST2 Heparan sulfate 6-O- 0.153 Xq26.2 Plays a role in growth sulfotransferase 2 (HS6ST2) factor signaling, cell adhesion, and enzymatic catalysis. Maybe involved in vascularization by mediating FGF signaling 4969 OGN Osteoglycin (osteoinductive 0.147 9q22 Regulates collagen factor, mimecan) (OGN), fibrillogenesis transcript variant 3 9687 GREB1 GREB1 protein, transcript 0.116 2p25.1 Transcription factor; variant a inhibits cell proliferation 6401 SELE Selectin E (endothelial 0.112 1q22-q25 Cell surface lycoprotein. adhesion molecule 1) (SELE) Inhibits cell adhesion. Early marker of inflammation 5350 PLN Phospholamban 0.108 6q22.1 Inhibits sarcoplasmic reticulum Ca(2+)- ATPase activity

TABLE 5 Genes specifically regulated in tumor endothelium. Fold difference ‘Parametric of geom means Gene p-value (Tumor/Normal) Probe set Description UG cluster symbol Map p < 1e−07 29.062 206026_s_at tumor necrosis factor, Hs.437322 TNFAIP6 2q23.3 alpha-induced protein 6 (TNFAIP6), mRNA. p < 1e−07 0.274 213803_at Karyopherin (importin) Hs.532793 KPNB1 17q21.32 beta 1 p < 1e−07 0.205 235309_at CDNA clone Hs.526499 16 IMAGE: 4140029   1e−007 2.85 228204_at proteasome (prosome, Hs.89545 PSMB4 1q21 macropain) subunit, beta type, 4 (PSMB4), mRNA.   1e−007 13.144 211597_s_at homeodomain-only Hs.121443 HOP 4q11-q12 protein (HOP), transcript variant 2, mRNA.   2e−007 3.116 213848_at Dual specificity Hs.3843 DUSP7 3p21 phosphatase 7   3e−007 3.599 233274_at NCK adaptor protein 1 Hs.477693 NCK1 3q21   3e−007 0.266 212653_s_at EH domain binding Hs.271667 EHBP1 2p15 protein 1 (EHBP1), mRNA.   4e−007 10.215 214081_at plexin domain containing Hs.125036 PLXDC1 17q21.1 1 (PLXDC1), mRNA.   4e−007 0.27 213364_s_at sorting nexin 1 (SNX1), Hs.188634 SNX1 15q22.31 transcript variant 2, mRNA.   4e−007 36.848 219454_at EGF-like-domain, Hs.12844 EGFL6 Xp22 multiple 6 (EGFL6), mRNA.   4e−007 18.969 213943_at twist homolog 1 Hs.66744 TWIST1 7p21.2 (acrocephalosyndactyly 3; Saethre-Chotzen syndrome) (Drosophila) (TWIST1), mRNA.   4e−007 0.327 225123_at Sestrin 3 Hs.120633 SESN3 11q21   5e−007 0.165 230081_at phosphatidylinositol- Hs.145404 PLCXD3 5p13.1 specific phospholipase C, X domain containing 3 (PLCXD3), mRNA.   7e−007 5.249 228579_at Potassium voltage-gated Hs.374023 KCNQ3 8q24 channel, KQT-like subfamily, member 3   8e−007 6.199 213661_at regeneration associated Hs.55044 DKFZP586H2123 11p13 muscle protease (DKFZP586H2123), transcript variant 2, mRNA.   9e−007 6.701 219764_at frizzled homolog 10 Hs.31664 FZD10 12q24.33 (Drosophila) (FZD10), mRNA.   9e−007 3.38 212044_s_at ribosomal protein L27a Hs.523463 RPL27A 11p15 (RPL27A), mRNA.   1e−006 0.42 213574_s_at Karyopherin (importin) Hs.532793 KPNB1 17q21.32 beta 1  1.1e−006 7.684 219700_at plexin domain containing Hs.125036 PLXDC1 17q21.1 1 (PLXDC1), mRNA.  1.2e−006 0.294 222791_at round spermatid basic Hs.486285 RSBN1 1p13.2 protein 1 (RSBN1), mRNA.  1.2e−006 0.232 221589_s_at Aldehyde dehydrogenase Hs.293970 ALDH6A1 14q24.3 6 family, member A1  1.2e−006 7.724 204285_s_at phorbol-12-myristate-13- Hs.96 PMAIP1 18q21.32 acetate-induced protein 1 (PMAIP1), mRNA.  1.4e−006 10.546 204595_s_at stanniocalcin 1 (STC1), Hs.25590 STC1 8p21-p11.2 mRNA.  1.5e−006 3.695 225147_at pleckstrin homology, Hs.487479 PSCD3 7p22.1 Sec7 and coiled-coil domains 3 (PSCD3), mRNA.  1.5e−006 9.368 234723_x_at CDNA: FLJ21228 fis, Hs.306716 7 clone COL00739  1.5e−006 0.374 212498_at Membrane-associated Hs.432862 MARCH- 5p15.2 ring finger (C3HC4) 6 VI  1.5e−006 13.326 230746_s_at stanniocalcin 1 (STC1), Hs.25590 STC1 8p21-p11.2 mRNA.  1.6e−006 6.09 219358_s_at centaurin, alpha 2 Hs.514063 CENTA2 17q11.2 (CENTA2), mRNA.  1.8e−006 0.346 201425_at aldehyde dehydrogenase Hs.436437 ALDH2 12q24.2 2 family (mitochondrial) (ALDH2), nuclear gene encoding mitochondrial protein, mRNA.  1.9e−006 4.094 225505_s_at chromosome 20 open Hs.29341 C20orf81 20p13 reading frame 81 (C20orf81), mRNA.  2.1e−006 0.284 219939_s_at cold shock domain Hs.69855 CSDE1 1p22 containing E1, RNA- binding (CSDE1), transcript variant 2, mRNA.  2.2e−006 4.136 221059_s_at coactosin-like 1 Hs.289092 COTL1 16q24.1 (Dictyostelium) (COTL1), mRNA.  2.2e−006 6.649 218856_at tumor necrosis factor Hs.443577 TNFRSF21 6p21.1-12.2 receptor superfamily, member 21 (TNFRSF21), mRNA.  2.4e−006 3.826 205068_s_at Rho GTPase activating Hs.293593 ARHGAP26 5q31 protein 26 (ARHGAP26), mRNA.  2.4e−006 4.807 242100_at chondroitin sulfate Hs.213137 CSS3 5q23.3 synthase 3 (CSS3), mRNA.  2.4e−006 5.981 206377_at forkhead box F2 Hs.484423 FOXF2 6p25.3 (FOXF2), mRNA.  2.4e−006 0.327 234512_x_at PREDICTED: similar to Hs.535174 LOC442159 6 Rpl7a protein (LOC442159), mRNA.  2.6e−006 4.037 232304_at Pellino homolog 1 Hs.7886 PELI1 2p13.3 (Drosophila)  2.7e−006 5.391 242546_at LOC440156 Hs.529095 14q11.1  2.7e−006 3.362 227295_at IKK interacting protein Hs.252543 IKIP 12q23.1 (IKIP), transcript variant 3.1, mRNA.  2.8e−006 4.563 1553575_at Unknown  2.9e−006 3.761 214924_s_at OGT(O-Glc-NAc Hs.535711 OIP106 3p25.3-p24.1 transferase)-interacting protein 106 KDa (OIP106), mRNA.   3e−006 6.144 242398_x_at WD repeat domain 77 Hs.204773 MEP50 1p13.2  3.5e−006 8.543 204286_s_at phorbol-12-myristate-13- Hs.96 PMAIP1 18q21.32 acetate-induced protein 1 (PMAIP1), mRNA.  3.7e−006 3.271 241632_x_at ESTs  3.9e−006 0.258 209512_at hydroxysteroid Hs.59486 HSDL2 9q32 dehydrogenase like 2 (HSDL2), mRNA.   4e−006 4.384 219359_at hypothetical protein Hs.353181 FLJ22635 11p15.5 FLJ22635 (FLJ22635), mRNA.   4e−006 0.279 227719_at CDNA FLJ37828 fis, Hs.123119 13 clone BRSSN2006575   4e−006 3.268 226063_at vav 2 oncogene (VAV2), Hs.369921 VAV2 9q34.1 mRNA.   4e−006 8.744 205269_at lymphocyte cytosolic Hs.304475 LCP2 5q33.1-qter protein 2 (SH2 domain containing leukocyte protein of 76 kDa) (LCP2), mRNA.  4.1e−006 3.906 215599_at SMA4 Hs.482411 SMA4 5q13  4.2e−006 0.434 214527_s_at polyglutamine binding protein 1 PQBP1 Xp11.23 (PQBP1), transcript variant 5, mRNA.  4.5e−006 4.068 220817_at transient receptor Hs.262960 TRPC4 13q13.1-q13.2 potential cation channel, subfamily C, member 4 (TRPC4), mRNA.  4.6e−006 0.237 202920_at ankyrin 2, neuronal Hs.137367 ANK2 4q25-q27 (ANK2), transcript variant 2, mRNA.  4.8e−006 6.865 209596_at matrix-remodelling Hs.369422 MXRA5 Xp22.33 associated 5 (MXRA5), mRNA.  5.1e−006 0.324 201737_s_at membrane-associated Hs.432862 38417 5p15.2 ring finger (C3HC4) 6 (MARCH6), mRNA.  5.3e−006 0.256 224763_at ribosomal protein L37 Hs.80545 RPL37 5p13 (RPL37), mRNA.  5.4e−006 6.857 212624_s_at chimerin (chimaerin) 1 Hs.380138 CHN1 2q31-q32.1 (CHN1), transcript variant 2, mRNA.  5.8e−006 0.203 222486_s_at ADAM metallopeptidase Hs.534115 ADAMTS1 21q21.2 with thrombospondin type 1 motif, 1 (ADAMTS1), mRNA.  5.9e−006 0.294 202908_at Wolfram syndrome 1 Hs.518602 WFS1 4p16 (wolframin) (WFS1), mRNA.  6.2e−006 0.267 242051_at Transcribed locus Hs.130260 X  6.3e−006 0.376 205412_at acetyl-Coenzyme A Hs.232375 ACAT1 11q22.3-q23.1 acetyltransferase 1 (acetoacetyl Coenzyme A thiolase) (ACAT1), nuclear gene encoding mitochondrial protein, mRNA.  6.5e−006 7.988 224549_x_at  6.8e−006 0.253 213272_s_at promethin (LOC57146), Hs.258212 LOC57146 16p12 mRNA.  7.2e−006 4.12 242369_x_at Nuclear receptor Hs.446678 NCOA2 8q13.3 coactivator 2  7.3e−006 0.26 226625_at Transforming growth Hs.482390 TGFBR3 1p33-p32 factor, beta receptor III (betaglycan, 300 kDa)  7.7e−006 0.245 219511_s_at synuclein, alpha Hs.426463 SNCAIP 5q23.1-q23.3 interacting protein (synphilin) (SNCAIP), mRNA.  7.8e−006 4.059 222449_at transmembrane, prostate Hs.517155 TMEPAI 20q13.31-q13.33 androgen induced RNA (TMEPAI), transcript variant 3, mRNA.   8e−006 2.237 212351_at eukaryotic translation Hs.283551 EIF2B5 3q27.1 initiation factor 2B, subunit 5 epsilon, 82 kDa (EIF2B5), mRNA.  8.1e−006 3.836 219634_at carbohydrate (chondroitin Hs.17569 CHST11 12q 4) sulfotransferase 11 (CHST11), mRNA.  8.3e−006 0.418 226751_at chromosome 2 open Hs.212885 C2orf32 2p14 reading frame 32 (C2orf32), mRNA.  8.3e−006 5.037 209081_s_at collagen, type XVIII, Hs.517356 COL18A1 21q22.3 alpha 1 (COL18A1), transcript variant 2, mRNA.   9e−006 2.362 205812_s_at transmembrane emp24 Hs.279929 TMED9 5q35.3 protein transport domain containing 9 (TMED9), mRNA.  9.3e−006 2.862 234985_at Hypothetical protein Hs.205865 LOC143458 11p13 LOC143458  9.6e−006 3.652 242029_at Fibronectin type III Hs.159430 FNDC3B 3q26.31 domain containing 3B  9.6e−006 0.386 211666_x_at ribosomal protein L3 Hs.119598 RPL3 22q13 (RPL3), mRNA.  9.8e−006 4.815 202465_at procollagen C- Hs.202097 PCOLCE 7q22 endopeptidase enhancer (PCOLCE), mRNA. 1.06e−005 0.303 203799_at CD302 antigen (CD302), Hs.130014 CD302 2q24.2 mRNA.  1.1e−005 3.787 228253_at lysyl oxidase-like 3 Hs.469045 LOXL3 2p13 (LOXL3), mRNA.  1.1e−005 3.674 209685_s_at protein kinase C, beta 1 Hs.460355 PRKCB1 16p11.2 (PRKCB1), transcript variant 2, mRNA. 1.11e−005 0.33 224445_s_at zinc finger, FYVE Hs.549192 ZFYVE21 14q32.33 domain containing 21 (ZFYVE21), mRNA. 1.13e−005 3.466 222379_at Potassium voltage-gated Hs.348522 KCNE4 2q36.3 channel, Isk-related family, member 4 1.15e−005 6.118 52255_s_at collagen, type V, alpha 3 Hs.235368 COL5A3 19p13.2 (COL5A3), mRNA. 1.17e−005 2.821 233180_at Ring finger protein 152 Hs.465316 RNF152 18q21.33 1.18e−005 0.232 212224_at aldehyde dehydrogenase Hs.76392 ALDH1A1 9q21.13 1 family, member A1 (ALDH1A1), mRNA.  1.2e−005 6.095 213350_at ribosomal protein S11 Hs.433529 RPS11 19q13.3 (RPS11), mRNA.  1.2e−005 3.729 226911_at hypothetical protein Hs.20103 FLJ39155 5p13.2-p13.1 FLJ39155 (FLJ39155), transcript variant 4, mRNA. 1.21e−005 2.975 219102_at reticulocalbin 3, EF-hand Hs.439184 RCN3 19q13.33 calcium binding domain (RCN3), mRNA. 1.25e−005 0.115 222722_at osteoglycin Hs.109439 OGN 9q22 (osteoinductive factor, mimecan) (OGN), transcript variant 3, mRNA. 1.29e−005 0.17 227703_s_at synaptotagmin-like 4 Hs.522054 SYTL4 Xq21.33 (granuphilin-a) (SYTL4), mRNA.  1.3e−005 0.46 211988_at SWI/SNF related, matrix Hs.463010 SMARCE1 17q21.2 associated, actin dependent regulator of chromatin, subfamily e, member 1 (SMARCE1), mRNA. 1.31e−005 0.238 204793_at G protein-coupled Hs.522730 GPRASP1 Xq22.1 receptor associated sorting protein 1 (GPRASP1), mRNA. 1.34e−005 0.339 229891_x_at KIAA1704 Hs.507922 KIAA1704 13q13-q14 1.35e−005 0.215 228554_at MRNA; cDNA Hs.32405 11 DKFZp586G0321 (from clone DKFZp586G0321) 1.38e−005 0.299 210950_s_at farnesyl-diphosphate Hs.546253 FDFT1 8p23.1-p22 farnesyltransferase 1 (FDFT1), mRNA. 1.38e−005 4.593 220014_at mesenchymal stem cell Hs.157461 LOC51334 5q23.1 protein DSC54 (LOC51334), mRNA.  1.4e−005 0.262 225162_at SH3 domain protein D19 Hs.519018 SH3D19 4q31.3 (SH3D19), mRNA. 1.41e−005 0.387 212408_at torsin A interacting Hs.496459 TOR1AIP1 1q24.2 protein 1 (TOR1AIP1), mRNA. 1.41e−005 0.446 201054_at heterogeneous nuclear Hs.96996 HNRPA0 5q31 ribonucleoprotein A0 (HNRPA0), mRNA. 1.47e−005 4.235 204639_at adenosine deaminase Hs.407135 ADA 20q12-q13.11 (ADA), mRNA.  1.5e−005 4.351 225646_at cathepsin C (CTSC), transcript variant 2, CTSC 11q14.1-q14.3 mRNA. 1.51e−005 3.657 209969_s_at signal transducer and Hs.470943 STAT1 2q32.2 activator of transcription 1, 91 kDa (STAT1), transcript variant beta, mRNA. 1.54e−005 2.663 236249_at IKK interacting protein Hs.252543 IKIP 12q23.1 (IKIP), transcript variant 1, mRNA. 1.58e−005 3.274 218804_at transmembrane protein Hs.503074 TMEM16A 11q13.3 16A (TMEM16A), mRNA. 1.59e−005 0.427 221988_at Hypothetical protein Hs.356467 MGC2747 19p13.11 MGC2747 1.59e−005 2.779 204786_s_at interferon (alpha, beta Hs.549042 IFNAR2 21q22.11 and omega) receptor 2 (IFNAR2), transcript variant 1, mRNA. 1.61e−005 0.413 200023_s_at eukaryotic translation Hs.516023 EIF3S5 11p15.4 initiation factor 3, subunit 5 epsilon, 47 kDa (EIF3S5), mRNA. 1.62e−005 4.278 201596_x_at keratin 18 (KRT18), Hs.406013 KRT18 12q13 transcript variant 2, mRNA. 1.64e−005 0.32 222605_at REST corepressor 3 Hs.356399 RCOR3 1q32.3 (RCOR3), mRNA. 1.64e−005 0.371 209733_at Hypothetical protein Hs.348844 LOC286440 Xq22.3 LOC286440 1.67e−005 4.144 232458_at Collagen, type III, alpha Hs.443625 COL3A1 2q31 1 (Ehlers-Danlos syndrome type IV, autosomal dominant)  1.7e−005 0.282 224901_at Stearoyl-CoA desaturase 5 Hs.379191 SCD4 4q21.3 1.73e−005 4.385 233912_x_at ELMO domain Hs.450105 ELMOD2 4q31.21 containing 2 1.76e−005 5.792 220301_at chromosome 18 open Hs.280781 C18orf14 18q22.1 reading frame 14 (C18orf14), mRNA. 1.76e−005 0.388 207170_s_at LETM1 domain Hs.370457 LETMD1 12q13.12 containing 1 (LETMD1), transcript variant 3, mRNA. 1.82e−005 0.418 201076_at NHP2 non-histone Hs.182255 NHP2L1 22q13.2-q13.31 chromosome protein 2- like 1 (S. cerevisiae) (NHP2L1), transcript variant 2, mRNA. 1.82e−005 0.252 228885_at MAM domain containing Hs.127386 MAMDC2 9q21.11 2 (MAMDC2), mRNA. 1.85e−005 0.411 212609_s_at V-akt murine thymoma Hs.498292 AKT3 1q43-q44 viral oncogene homolog 3 (protein kinase B, gamma) 1.86e−005 4.564 221558_s_at lymphoid enhancer- Hs.555947 LEF1 4q23-q25 binding factor 1 (LEF1), mRNA. 1.87e−005 3.054 235204_at Ectonucleoside Hs.369424 ENTPD7 10 triphosphate diphosphohydrolase 7  1.9e−005 3.283 202820_at aryl hydrocarbon receptor Hs.171189 AHR 7p15 (AHR), mRNA. 1.91e−005 4.787 1565823_at septin 7 (SEPT7), Hs.191346 38602 7p14.3-p14.1 transcript variant 2 mRNA. 1.93e−005 0.342 221726_at ribosomal protein L22 Hs.515329 RPL22 1p36.3-p36.2 (RPL22), mRNA. 1.93e−005 0.485 202029_x_at ribosomal protein L38 Hs.380953 RPL38 17q23-q25 (RPL38), mRNA. 1.94e−005 0.258 209513_s_at hydroxysteroid Hs.59486 HSDL2 9q32 dehydrogenase like 2 (HSDL2), mRNA. 1.95e−005 0.356 226806_s_at MRNA; cDNA Hs.379253 1 DKFZp686J23256 (from clone DKFZp686J23256) 2.01e−005 4.146 1558048_x_at Unknown 2.03e−005 3.183 237494_at Transcribed locus Hs.174934 15 2.09e−005 0.306 201432_at catalase (CAT), mRNA. Hs.502302 CAT 11p13 2.11e−005 3.698 203878_s_at matrix metallopeptidase Hs.143751 MMP11 22q11.23 11 (stromelysin 3) (MMP11), mRNA. 2.11e−005 2.481 212323_s_at vacuolar protein sorting Hs.439381 VPS13D 1p36.22-p36.21 13D (yeast) (VPS13D), transcript variant 2, mRNA. 2.11e−005 0.215 242488_at CDNA FLJ38396 fis, Hs.155736 1 clone FEBRA2007957 2.14e−005 2.201 219092_s_at chromosome 9 open Hs.16603 C9orf12 9q21.33-q22.31 reading frame 12 (C9orf12), mRNA. 2.15e−005 2.239 217118_s_at chromosome 22 open Hs.369682 C22orf9 22q13.31 reading frame 9 (C22orf9), transcript variant 2, mRNA. 2.29e−005 0.44 214097_at Ribosomal protein S21 Hs.190968 RPS21 20q13.3 2.29e−005 5.232 225799_at hypothetical protein Hs.446688 MGC4677 2p11.2 MGC4677 (MGC4677), mRNA.  2.3e−005 3.258 244197_x_at CCR4-NOT transcription Hs.133350 CNOT2 12q15 complex, subunit 2 2.37e−005 7.605 202952_s_at ADAM metallopeptidase Hs.386283 ADAM12 10q26.3 domain 12 (meltrin alpha) (ADAM12), transcript variant 1, mRNA.  2.4e−005 0.462 201030_x_at lactate dehydrogenase B Hs.446149 LDHB 12p12.2-p12.1 (LDHB), mRNA. 2.41e−005 0.349 208643_s_at X-ray repair Hs.388739 XRCC5 2q35 complementing defective repair in Chinese hamster cells 5 (double-strand- break rejoining; Ku autoantigen, 80 kDa) (XRCC5), mRNA.  2.5e−005 0.381 200013_at ribosomal protein L24 Hs.477028 RPL24 3q12 (RPL24), mRNA. 2.57e−005 10.355 221731_x_at chondroitin sulfate Hs.443681 CSPG2 5q14.3 proteoglycan 2 (versican) (CSPG2), mRNA. 2.66e−005 0.175 211569_s_at L-3-hydroxyacyl- Hs.438289 HADHSC 4q22-q26 Coenzyme A dehydrogenase, short chain (HADHSC), mRNA. 2.69e−005 0.412 201023_at TAF7 RNA polymerase Hs.438838 TAF7 5q31 II, TATA box binding protein (TBP)-associated factor, 55 kDa (TAF7), mRNA. 2.71e−005 5.473 224254_x_at Transferrin Hs.518267 TF 3q22.1 2.75e−005 4.279 213479_at neuronal pentraxin II Hs.3281 NPTX2 7q21.3-q22.1 (NPTX2), mRNA. 2.81e−005 3.34 230440_at PREDICTED: zinc finger Hs.54925 ZNF469 16 protein 469 (ZNF469), mRNA. 2.86e−005 3.995 227347_x_at hairy and enhancer of Hs.154029 HES4 1p36.33 split 4 (Drosophila) (HES4), mRNA. 2.87e−005 2.894 218131_s_at GATA zinc finger Hs.118964 GATAD2A 19p13.11 domain containing 2A (GATAD2A), mRNA.  2.9e−005 0.327 235612_at Transcribed locus, Hs.396796 1 moderately similar to NP_858931.1 NFS1 nitrogen fixation 1 isoform b precursor; cysteine desulfurase; nitrogen-fixing bacteria S-like protein; nitrogen fixation 1 (S. cerevisiae, homolog) [Homo sapiens] 2.94e−005 0.186 229308_at Transcribed locus Hs.355689 18 3.01e−005 2.617 223617_x_at ATPase family, AAA Hs.23413 ATAD3B 1p36.33 domain containing 3B (ATAD3B), mRNA. 3.01e−005 4.273 240655_at Activated leukocyte cell Hs.150693 ALCAM 3q13.1 adhesion molecule 3.07e−005 2.553 209030_s_at immunoglobulin Hs.370510 IGSF4 11q23.2 superfamily, member 4 (IGSF4), mRNA. 3.07e−005 2.812 210069_at carnitine Hs.439777 CPT1B 22q13.33 palmitoyltransferase 1B (muscle) (CPT1B), nuclear gene encoding mitochondrial protein, transcript variant 3, mRNA.  3.1e−005 2.462 213258_at Tissue factor pathway Hs.516578 TFPI 2q31-q32.1 inhibitor (lipoprotein- associated coagulation inhibitor) 3.28e−005 4.4 241686_x_at ESTs, Weakly similar to hypothetical protein FLJ20378 [Homo sapiens] [H. sapiens] 3.33e−005 5.315 1553186_x_at RAS and EF-hand Hs.129136 RASEF 9q21.32 domain containing 3.34e−005 0.361 226280_at BCL2/adenovirus E1B Hs.283454 BNIP2 15q22.2 19 kDa interacting protein 2 3.34e−005 0.481 218929_at collaborates/cooperates Hs.32922 CARF 4q35.1 with ARF (alternate reading frame) protein (CARF), mRNA. 3.36e−005 2.651 61734_at Reticulocalbin 3, EF- Hs.439184 RCN3 19q13.33 hand calcium binding domain 3.38e−005 3.492 204735_at phosphodiesterase 4A, Hs.89901 PDE4A 19p13.2 cAMP-specific (phosphodiesterase E2 dunce homolog, Drosophila) (PDE4A), mRNA.  3.4e−005 4.417 47550_at leucine zipper, putative Hs.521432 LZTS1 8p22 tumor suppressor 1 (LZTS1), mRNA. 3.41e−005 0.309 225698_at TIGA1 (TIGA1), mRNA. Hs.12082 TIGA1 5q21-q22 3.42e−005 0.304 211986_at AHNAK nucleoprotein Hs.502756 AHNAK 11q12.2 (desmoyokin) (AHNAK), transcript variant 1, mRNA. 3.43e−005 0.31 225387_at Tetraspanin 5 Hs.118118 TM4SF9 4q23 3.48e−005 0.442 201600_at prohibitin 2 (PHB2), Hs.504620 PHB2 12p13 mRNA.  3.5e−005 0.323 225125_at transmembrane protein Hs.110702 TMEM32 Xq26.3 32 (TMEM32), mRNA. 3.52e−005 4.82 206637_at purinergic receptor P2Y, Hs.2465 P2RY14 3q21-q25 G-protein coupled, 14 (P2RY14), mRNA.  3.6e−005 0.475 221725_at WAS protein family, Hs.469244 WASF2 1p36.11-p34.3 member 2 3.63e−005 0.387 209385_s_at proline synthetase co- Hs.304792 PROSC 8p11.2 transcribed homolog (bacterial) (PROSC), mRNA. 3.65e−005 2.247 218018_at pyridoxal (pyridoxine, Hs.284491 PDXK 21q22.3 vitamin B6) kinase (PDXK), mRNA. 3.68e−005 2.36 224598_at mannosyl (alpha-1,3-)- Hs.437277 MGAT4B 5q35 glycoprotein beta-1,4-N- acetylglucosaminyltransferase, isoenzyme B (MGAT4B), transcript variant 1, mRNA. 3.71e−005 0.502 225489_at transmembrane protein Hs.43899 TMEM18 2p25.3 18 (TMEM18), mRNA. 3.72e−005 0.264 239262_at CDNA FLJ26242 fis, Hs.377660 11 clone DMC00770 3.75e−005 0.277 226184_at formin-like 2 (FMNL2), Hs.149566 FMNL2 2q23.3 transcript variant 2, mRNA. 3.77e−005 0.251 228027_at G protein-coupled Hs.348493 GPRASP2 Xq22.1 receptor associated sorting protein 2 (GPRASP2), transcript variant 2, mRNA. 3.79e−005 0.257 203803_at prenylcysteine oxidase 1 Hs.551542 PCYOX1 2p13.3 (PCYOX1), mRNA. 3.79e−005 6.76 213418_at heat shock 70 kDa protein Hs.3268 HSPA6 1q23 6 (HSP70B′) (HSPA6), mRNA. 3.82e−005 2.139 1556242_a_at Homo sapiens, clone Hs.547780 8 IMAGE: 3885623, mRNA 3.84e−005 0.407 209447_at spectrin repeat Hs.12967 SYNE1 6q25 containing, nuclear envelope 1 (SYNE1), transcript variant alpha, mRNA. 3.89e−005 0.367 213900_at chromosome 9 open Hs.118003 C9orf61 9q13-q21 reading frame 61 (C9orf61), mRNA. 3.91e−005 2.496 205406_s_at sperm autoantigenic Hs.286233 SPA17 11q24.2 protein 17 (SPA17), mRNA. 3.91e−005 2.719 213344_s_at H2A histone family, Hs.477879 H2AFX 11q23.2-q23.3 member X (H2AFX), mRNA. 3.95e−005 0.318 228551_at Hypothetical protein Hs.118166 MGC24039 12p11.21 MGC24039 3.96e−005 4.16 235343_at Hypothetical protein Hs.96885 FLJ12505 1q32.3 FLJ12505 4.04e−005 5.126 209082_s_at collagen, type XVIII, Hs.517356 COL18A1 21q22.3 alpha 1 (COL18A1), transcript variant 2, mRNA. 4.15e−005 0.476 230958_s_at MRNA; cDNA Hs.379253 1 DKFZp686J23256 (from clone DKFZp686J23256) 4.17e−005 0.38 219054_at hypothetical protein Hs.13528 FLJ14054 5p13.3 FLJ14054 (FLJ14054), mRNA.  4.2e−005 0.358 208951_at aldehyde dehydrogenase Hs.483239 ALDH7A1 5q31 7 family, member A1 (ALDH7A1), mRNA.  4.2e−005 4.533 205241_at SCO cytochrome oxidase Hs.549099 SCO2 22q13.33 deficient homolog 2 (yeast) (SCO2), nuclear gene encoding mitochondrial protein, mRNA. 4.23e−005 0.434 218528_s_at ring finger protein 38 Hs.333503 RNF38 9p13-p12 (RNF38), transcript variant 4, mRNA. 4.28e−005 0.489 212131_at family with sequence Hs.407368 FAM61A 19q13.11 similarity 61, member A (FAM61A), mRNA. 4.45e−005 0.365 225546_at Eukaryotic elongation Hs.549151 EEF2K 16p12.1 factor-2 kinase 4.45e−005 0.237 229145_at chromosome 10 open Hs.426296 C10orf104 10q22.1 reading frame 104 (C10orf104), mRNA. 4.47e−005 0.387 227273_at Transcribed locus Hs.483955 10 4.48e−005 3.428 220575_at hypothetical protein Hs.287456 FLJ11800 17p11.2 FLJ11800 (FLJ11800), mRNA. 4.49e−005 0.379 202073_at optineurin (OPTN), Hs.332706 OPTN 10p13 transcript variant 2, mRNA. 4.54e−005 4.845 1559436_x_at Arrestin, beta 2 Hs.435811 ARRB2 17p13 4.54e−005 4.79 220232_at stearoyl-CoA desaturase Hs.379191 SCD5 4q21.3 5 (SCD5), mRNA. 4.59e−005 5.647 233330_s_at Similar to Ribosome Hs.455494 9q13 biogenesis protein BMS1 homolog 4.66e−005 3.575 1559410_at Unknown 4.67e−005 0.425 211769_x_at tumor differentially Hs.272168 TDE1 20q13.1-13.3 expressed 1 (TDE1), transcript variant 1, mRNA. 4.85e−005 0.443 226529_at hypothetical protein Hs.396358 FLJ11273 7p21.3 FLJ11273 (FLJ11273), mRNA. 4.85e−005 0.413 208697_s_at eukaryotic translation Hs.405590 EIF3S6 8q22-q23 initiation factor 3, subunit 6 48 kDa (EIF3S6), mRNA. 4.85e−005 0.404 225050_at zinc finger protein 512 Hs.529178 ZNF512 2p23 (ZNF512), mRNA.  4.9e−005 0.277 208704_x_at amyloid beta (A4) Hs.370247 APLP2 11q24 precursor-like protein 2 (APLP2), mRNA. 5.08e−005 0.501 202502_at acyl-Coenzyme A Hs.445040 ACADM 1p31 dehydrogenase, C-4 to C- 12 straight chain (ACADM), nuclear gene encoding mitochondrial protein, mRNA.  5.1e−005 2.907 223276_at putative small membrane Hs.29444 NID67 5q33.1 protein NID67 (NID67), mRNA.  5.1e−005 0.484 208873_s_at chromosome 5 open Hs.429608 C5orf18 5q22-q23 reading frame 18 (C5orf18), mRNA. 5.11e−005 2.383 46665_at sema domain, Hs.516220 SEMA4C 2q11.2 immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C (SEMA4C), mRNA. 5.16e−005 3 1559060_a_at KIAA1961 gene Hs.483329 KIAA1961 5q23.3 5.29e−005 2.423 215577_at Ubiquitin-conjugating Hs.164853 UBE2E1 3p24.2 enzyme E2E 1 (UBC4/5 homolog, yeast) 5.29e−005 4.015 222252_x_at leucine rich repeat Hs.317243 LRRC51 11q13.4 containing 51 (LRRC51), mRNA. 5.35e−005 0.284 208248_x_at amyloid beta (A4) Hs.370247 APLP2 11q24 precursor-like protein 2 (APLP2), mRNA. 5.35e−005 3.191 1558836_at MRNA; cDNA Hs.157344 2 DKFZp667A182 (from clone DKFZp667A182) 5.35e−005 0.538 209066_x_at ubiquinol-cytochrome c Hs.131255 UQCRB 8q22 reductase binding protein (UQCRB), mRNA. 5.39e−005 4.851 226777_at A disintegrin and Hs.386283 ADAM12 10q26.3 metalloproteinase domain 12 (meltrin alpha)  5.4e−005 0.459 208990_s_at heterogeneous nuclear Hs.499891 HNRPH3 10q22 ribonucleoprotein H3 (2H9) (HNRPH3), transcript variant 2H9A, mRNA. 5.42e−005 3.146 235122_at CDNA clone Hs.403972 1 IMAGE: 6254031 5.44e−005 2.185 59433_at Transcribed locus Hs.416792 X 5.44e−005 0.473 225811_at Transcribed locus, Hs.78050 11 weakly similar to XP_510104.1 PREDICTED: similar to hypothetical protein FLJ25224 [Pan troglodytes] 5.53e−005 0.39 200760_s_at ADP-ribosylation-like Hs.518060 ARL6IP5 3p14 factor 6 interacting protein 5 (ARL6IP5), mRNA. 5.55e−005 4.287 219025_at CD248 antigen, Hs.195727 CD248 11q13 endosialin (CD248), mRNA. 5.65e−005 3.458 211673_s_at Molybdenum cofactor Hs.357128 MOCS1 6p21.3 synthesis 1 5.75e−005 2.33 225947_at myosin head domain Hs.302051 MYOHD1 17q12 containing 1 (MYOHD1), mRNA. 5.78e−005 0.468 225332_at Keratin associated protein Hs.549512 KRTAP4-7 17q12-q21 4-7 5.79e−005 3.761 226933_s_at inhibitor of DNA binding Hs.519601 ID4 6p22-p21 4, dominant negative helix-loop-helix protein (ID4), mRNA. 5.83e−005 0.421 200937_s_at ribosomal protein L5 Hs.532359 RPL5 1p22.1 (RPL5), mRNA. 5.92e−005 4.185 219263_at ring finger protein 128 Hs.496542 RNF128 Xq22.3 (RNF128), transcript variant 2, mRNA. 5.98e−005 2.652 224967_at UDP-glucose ceramide Hs.304249 UGCG 9q31 glucosyltransferase 5.98e−005 2.885 222968_at chromosome 6 open Hs.109798 C6orf48 6p21.3 reading frame 48 (C6orf48), mRNA. 6.02e−005 4.748 238673_at Transcribed locus Hs.359393 8 6.02e−005 0.418 223306_at emopamil binding Hs.433278 EBPL 13q12-q13 protein-like (EBPL), mRNA. 6.09e−005 2.563 238327_at Similar to MGC52679 Hs.531314 22q13.33 protein 6.11e−005 0.341 227728_at Protein phosphatase 1A Hs.130036 PPM1A 14q23.1 (formerly 2C), magnesium-dependent, alpha isoform 6.17e−005 0.212 205466_s_at heparan sulfate Hs.507348 HS3ST1 4p16 (glucosamine) 3-O- sulfotransferase 1 (HS3ST1), mRNA. 6.24e−005 0.452 202512_s_at APG5 autophagy 5-like Hs.486063 APG5L 6q21 (S. cerevisiae) (APG5L), mRNA. 6.25e−005 2.159 202297_s_at RER1 retention in Hs.525527 RER1 1pter-q24 endoplasmic reticulum 1 homolog (S. cerevisiae) (RER1), mRNA. 6.29e−005 5.165 242862_x_at ESTs 6.34e−005 0.41 234339_s_at glioma tumor suppressor Hs.421907 GLTSCR2 19q13.3 candidate region gene 2 (GLTSCR2), mRNA. 6.38e−005 3.706 215588_x_at RIO kinase 3 (yeast) Hs.445511 RIOK3 18q11.2 6.45e−005 0.446 202378_s_at leptin receptor Hs.23581 LEPROT 1p31.2 overlapping transcript (LEPROT), mRNA. 6.52e−005 4.272 234675_x_at CDNA: FLJ23566 fis, Hs.532596 14 clone LNG10880 6.61e−005 2.48 200734_s_at ADP-ribosylation factor 3 Hs.119177 ARF3 12q13 (ARF3), mRNA. 6.64e−005 0.373 202630_at amyloid beta precursor Hs.84084 APPBP2 17q21-q23 protein (cytoplasmic tail) binding protein 2 (APPBP2), mRNA. 6.64e−005 0.417 212549_at signal transducer and Hs.132864 STAT5B 17q11.2 activator of transcription 5B (STAT5B), mRNA. 6.66e−005 0.332 235072_s_at Transcribed locus Hs.94499 6 6.72e−005 0.441 201535_at ubiquitin-like 3 (UBL3), Hs.145575 UBL3 13q12-q13 mRNA. 6.79e−005 2.242 224612_s_at DnaJ (Hsp40) homolog, Hs.164419 DNAJC5 20q13.33 subfamily C, member 5  6.8e−005 4.528 215179_x_at Placental growth factor, Hs.252820 PGF 14q24-q31 vascular endothelial growth factor-related protein 6.81e−005 0.361 218191_s_at LMBR1 domain Hs.271643 LMBRD1 6q13 containing 1 (LMBRD1), mRNA. 6.82e−005 3.714 206792_x_at phosphodiesterase 4C, Hs.437211 PDE4C 19p13.11 cAMP-specific (phosphodiesterase E1 dunce homolog, Drosophila) (PDE4C), mRNA. 6.85e−005 2.964 44783_s_at hairy/enhancer-of-split Hs.234434 HEY1 8q21 related with YRPW motif 1 (HEY1), mRNA. 7.02e−005 0.354 211942_x_at Ribosomal protein L13a Hs.546356 RPL13A 19q13.3 7.05e−005 3.112 222358_x_at ESTs, Weakly similar to hypothetical protein FLJ20378 [Homo sapiens] [H. sapiens] 7.05e−005 0.387 203427_at ASF1 anti-silencing Hs.292316 ASF1A 6q22.31 function 1 homolog A (S. cerevisiae) (ASF1A), mRNA. 7.12e−005 5.701 243147_x_at ESTs, Weakly similar to RMS1_HUMAN REGULATOR OF MITOTIC SPINDLE ASSEMBLY 1 [H. sapiens] 7.15e−005 5.24 1554334_a_at DnaJ (Hsp40) homolog, Hs.513053 DNAJA4 15q25.1 subfamily A, member 4 (DNAJA4), mRNA. 7.18e−005 3.411 204136_at collagen, type VII, alpha Hs.476218 COL7A1 3p21.1 1 (epidermolysis bullosa, dystrophic, dominant and recessive) (COL7A1), mRNA. 7.19e−005 0.308 200883_at ubiquinol-cytochrome c Hs.528803 UQCRC2 16p12 reductase core protein II (UQCRC2), mRNA. 7.21e−005 2.399 243249_at ESTs, Weakly similar to hypothetical protein FLJ20378 [Homo sapiens] [H. sapiens] 7.25e−005 0.412 218167_at archaemetzincins-2 Hs.268122 AMZ2 17q24.2 (AMZ2), mRNA. 7.26e−005 4.893 234578_at MRNA; cDNA Hs.537604 1 DKFZp434E1812 (from clone DKFZp434E1812) 7.26e−005 2.797 203349_s_at ets variant gene 5 (ets- Hs.43697 ETV5 3q28 related molecule) (ETV5), mRNA. 7.32e−005 2.605 212809_at nuclear factor of Hs.513470 NFATC2IP 16p11.2 activated T-cells, cytoplasmic, calcineurin- dependent 2 interacting protein (NFATC2IP), mRNA. 7.34e−005 0.32 230793_at leucine rich repeat Hs.116470 LRRC16 6p22.2 containing 16 (LRRC16), mRNA. 7.35e−005 0.448 203897_at hypothetical protein A- Hs.185489 LOC57149 16p11.2 211C6.1 (LOC57149), mRNA. 7.37e−005 3.381 241718_x_at ESTs  7.4e−005 0.451 208740_at sin3-associated Hs.524899 SAP18 13q12.11 polypeptide, 18 kDa (SAP18), mRNA. 7.41e−005 0.392 211749_s_at vesicle-associated Hs.66708 VAMP3 1p36.23 membrane protein 3 (cellubrevin) (VAMP3), mRNA. 7.44e−005 4.754 209360_s_at runt-related transcription Hs.149261 RUNX1 21q22.3 factor 1 (acute myeloid leukemia 1; aml1 oncogene) (RUNX1), transcript variant 1, mRNA. 7.45e−005 0.461 225498_at chromatin modifying Hs.472471 CHMP4B 20q11.22 protein 4B (CHMP4B), mRNA. 7.51e−005 4.374 213790_at A disintegrin and Hs.386283 ADAM12 10q26.3 metalloproteinase domain 12 (meltrin alpha) 7.57e−005 2.898 230270_at ESTs 7.64e−005 0.321 219023_at chromosome 4 open Hs.435991 C4orf16 4q25 reading frame 16 (C4orf16), mRNA. 7.65e−005 0.116 205862_at GREB1 protein Hs.467733 GREB1 2p25.1 (GREB1), transcript variant a, mRNA. 7.86e−005 4.771 217679_x_at ESTs, Weakly similar to hypothetical protein FLJ20489 [Homo sapiens] [H. sapiens] 7.88e−005 2.558 204387_x_at mitochondrial ribosomal Hs.458367 MRP63 13p11.1-q11 protein 63 (MRP63), nuclear gene encoding mitochondrial protein, mRNA. 7.89e−005 0.454 226020_s_at OMA1 homolog, zinc Hs.425769 OMA1 1p32.2-p32.1 metallopeptidase (S. cerevisiae) (OMA1), mRNA. 7.97e−005 2.379 214316_x_at Calreticulin Hs.515162 CALR 19p13.3-p13.2 7.99e−005 0.39 218831_s_at Fc fragment of IgG, Hs.111903 FCGRT 19q13.3 receptor, transporter, alpha (FCGRT), mRNA. 8.09e−005 3.577 208246_x_at hypothetical protein FLJ20006 FLJ20006 16q23.1 8.13e−005 3.611 231825_x_at Activating transcription Hs.546406 ATF7IP 12p13.1 factor 7 interacting protein 8.16e−005 2.701 236251_at Integrin, alpha V Hs.436873 ITGAV 2q31-q32 (vitronectin receptor, alpha polypeptide, antigen CD51) 8.18e−005 3.162 232617_at cathepsin S (CTSS), Hs.181301 CTSS 1q21 mRNA. 8.21e−005 2.949 31874_at Growth arrest-specific 2 Hs.322852 GAS2L1 22q12.2 like 1 8.32e−005 4.254 1566887_x_at KIAA0284 Hs.533721 KIAA0284 14q32.33 8.43e−005 0.475 226297_at ESTs 8.47e−005 0.458 227293_at Ligand of numb-protein X Hs.407755 LNX 4q12 8.47e−005 0.337 227530_at A kinase (PRKA) anchor Hs.371240 AKAP12 6q24-q25 protein (gravin) 12 8.52e−005 0.178 211276_at transcription elongation Hs.401835 TCEAL2 Xq22.1-q22.3 factor A (SII)-like 2 (TCEAL2), mRNA. 8.57e−005 0.489 208635_x_at nascent-polypeptide- Hs.505735 NACA 12q23-q24.1 associated complex alpha polypeptide (NACA), mRNA. 8.57e−005 0.416 225574_at hypothetical protein Hs.133337 MGC10198 4q35.1 MGC10198 (MGC10198), mRNA. 8.66e−005 3.115 244457_at Inositol 1,4,5- Hs.512235 ITPR2 12p11 triphosphate receptor, type 2 8.72e−005 0.373 226117_at TRAF-interacting protein Hs.310640 TIFA 4q25 with a forkhead- associated domain (TIFA), mRNA. 8.75e−005 4.112 234762_x_at Neurolysin Hs.247460 NLN 5q12.3 (metallopeptidase M3 family) 8.75e−005 2.496 232254_at F-box protein 25 Hs.438454 FBXO25 8p23.3 8.83e−005 3.223 1570061_at CDNA clone Hs.372904 3 IMAGE: 4555030 8.86e−005 0.372 220327_at vestigial-like 3 (VGL-3), Hs.435013 VGL-3 3p12.1 mRNA. 8.88e−005 0.501 225326_at PREDICTED: RNA Hs.61441 RBM27 5 binding motif protein 27 (RBM27), mRNA. 8.91e−005 0.347 215294_s_at SWI/SNF related, matrix Hs.152292 SMARCA1 Xq25 associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1), transcript variant 2, mRNA. 8.94e−005 3.111 242329_at PREDICTED: Hs.437075 LOC401317 7 hypothetical LOC401317 (LOC401317), mRNA. 8.97e−005 0.37 238613_at sterile alpha motif and Hs.444451 ZAK 2q24.2 leucine zipper containing kinase AZK (ZAK), transcript variant 2, mRNA. 8.97e−005 2.137 203459_s_at vacuolar protein sorting Hs.269577 VPS16 20p13-p12 16 (yeast) (VPS16), transcript variant 2, mRNA. 9.04e−005 5.612 215978_x_at ATP-binding cassette, Hs.478916 LOC152719 4p16.3 sub-family A (ABC1), member 11 (pseudogene) 9.1e−005 0.419 222488_s_at dynactin 4 (p62) Hs.328865 DCTN4 5q31-q32 (DCTN4), mRNA. 9.25e−005 0.449 217915_s_at chromosome 15 open Hs.274772 C15orf15 15q21 reading frame 15 (C15orf15), mRNA. 9.26e−005 3.027 204184_s_at adrenergic, beta, receptor Hs.517493 ADRBK2 22q12.1 kinase 2 (ADRBK2), mRNA. 9.35e−005 0.152 223395_at ABI gene family, Hs.477015 ABI3BP 3q12 member 3 (NESH) binding protein (ABI3BP), mRNA. 9.38e−005 3.287 206247_at MHC class I polypeptide- Hs.211580 MICB 6p21.3 related sequence B (MICB), mRNA. 9.41e−005 0.341 222975_s_at cold shock domain Hs.69855 CSDE1 1p22 containing E1, RNA- binding (CSDE1), transcript variant 2, mRNA. 9.42e−005 0.43 227407_at hypothetical protein Hs.479223 FLJ90013 4p15.32 FLJ90013 (FLJ90013), mRNA. 9.46e−005 0.424 223189_x_at myeloid/lymphoid or Hs.369356 MLL5 7q22.1 mixed-lineage leukemia 5 (trithorax homolog, Drosophila) (MLL5), mRNA. 9.63e−005 0.474 200735_x_at nascent-polypeptide- Hs.505735 NACA 12q23-q24.1 associated complex alpha polypeptide (NACA), mRNA. 9.73e−005 2.027 219099_at chromosome 12 open Hs.504545 C12orf5 12p13.3 reading frame 5 (C12orf5), mRNA. 9.74e−005 2.083 243_g_at microtubule-associated Hs.517949 MAP4 3p21 protein 4 (MAP4), transcript variant 2, mRNA. 9.85e−005 4.389 234981_x_at Similar to mouse Hs.192586 LOC134147 5p15.2 2310016A09Rik gene 9.87e−005 0.544 208756_at eukaryotic translation Hs.530096 EIF3S2 1p34.1 initiation factor 3, subunit 2 beta, 36 kDa (EIF3S2), mRNA. 0.0001001 3.738 243442_x_at ESTs, Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 0.0001002 4.754 223672_at SH3-domain GRB2-like Hs.132121 SGIP1 1p31.2 (endophilin) interacting protein 1 (SGIP1), mRNA. 0.0001004 3.899 230077_at Transferrin receptor (p90, Hs.529618 TFRC 3q29 CD71) 0.0001021 0.362 212215_at prolyl endopeptidase-like Hs.112916 PREPL 2p22.1 (PREPL), mRNA. 0.0001021 0.507 225098_at Abl interactor 2 Hs.471156 ABI2 2q33 0.0001023 0.556 218142_s_at cereblon (CRBN), Hs.18925 CRBN 3p26.2 mRNA. 0.0001027 0.445 214177_s_at pre-B-cell leukemia Hs.505806 PBXIP1 1q22 transcription factor interacting protein 1 (PBXIP1), mRNA. 0.0001028 0.227 208791_at clusterin (complement Hs.436657 CLU 8p21-p12 lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J) (CLU), transcript variant 1, mRNA. 0.0001035 2.522 200021_at cofilin 1 (non-muscle) Hs.170622 CFL1 11q13 (CFL1), mRNA. 0.0001036 3.432 229801_at chromosome 10 open Hs.435775 C10orf47 10p14 reading frame 47 (C10orf47), mRNA. 0.000105 0.303 212731_at ankyrin repeat domain 46 Hs.530199 ANKRD46 8q22.3 (ANKRD46), mRNA. 0.0001078 0.389 224841_x_at PREDICTED: RNA, U47 small nuclear RNU47 1 (RNU47), misc RNA. 0.0001087 0.419 228905_at Transcribed locus, Hs.554337 8 moderately similar to XP_517655.1 PREDICTED: similar to KIAA0825 protein [Pan troglodytes] 0.0001115 0.379 202314_at cytochrome P450, family Hs.417077 CYP51A1 7q21.2-q21.3 51, subfamily A, polypeptide 1 (CYP51A1), mRNA. 0.000112 0.169 200965_s_at actin binding LIM protein Hs.438236 ABLIM1 10q25 1 (ABLIM1), transcript variant 4, mRNA. 0.0001134 2.869 227850_x_at CDC42 effector protein Hs.415791 CDC42EP5 19q13.42 (Rho GTPase binding) 5 (CDC42EP5), mRNA. 0.0001136 0.451 211710_x_at ribosomal protein L4 Hs.432898 RPL4 15q22 (RPL4), mRNA. 0.000114 4.037 1562062_at Homo sapiens transcribed sequence with weak similarity to protein ref: NP_055301.1 (H. sapiens) neuronal thread protein [Homo sapiens] 0.0001144 0.403 224741_x_at Growth arrest-specific 5 Hs.531856 GAS5 1q23.3 0.0001149 0.503 224689_at mannosidase, beta A, Hs.6126 MANBAL 20q11.23-q12 lysosomal-like (MANBAL), transcript variant 2, mRNA. 0.0001159 0.449 201154_x_at ribosomal protein L4 Hs.432898 RPL4 15q22 (RPL4), mRNA. 0.0001171 0.243 202068_s_at low density lipoprotein Hs.213289 LDLR 19p13.3 receptor (familial hypercholesterolemia) (LDLR), mRNA. 0.0001172 0.438 226541_at F-box protein 30 Hs.421095 FBXO30 6q24 (FBXO30), mRNA. 0.0001174 2.25 229520_s_at Chromosome 14 open Hs.410231 C14orf118 14q22.1-q24.3 reading frame 118 0.0001175 0.224 208792_s_at clusterin (complement Hs.436657 CLU 8p21-p12 lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J) (CLU), transcript variant 1, mRNA. 0.0001184 0.438 212644_s_at chromosome 14 open Hs.437831 C14orf32 14q22.2-q22.3 reading frame 32 (C14orf32), mRNA. 0.0001189 0.207 212094_at PREDICTED: paternally Hs.147492 PEG10 7 expressed 10 (PEG10), mRNA. 0.0001207 7.544 204597_x_at stanniocalcin 1 (STC1), Hs.25590 STC1 8p21-p11.2 mRNA. 0.000121 0.518 201696_at splicing factor, Hs.469970 SFRS4 1p35.3 arginine/serine-rich 4 (SFRS4), mRNA. 0.0001224 3.248 231411_at lipoma HMGIC fusion Hs.507798 LHFP 13q12 partner (LHFP), mRNA. 0.0001224 0.45 203494_s_at translokin (PIG8), Hs.101014 PIG8 11q21 mRNA. 0.0001227 0.391 225243_s_at sarcolemma associated Hs.476432 SLMAP 3p21.2-p14.3 protein (SLMAP), mRNA. 0.0001234 2.695 203505_at ATP-binding cassette, Hs.429294 ABCA1 9q31.1 sub-family A (ABC1), member 1 0.000125 2.866 213146_at KIAA0346 protein KIAA0346 17p13.1 0.0001252 3.538 235205_at PREDICTED: similar to Hs.127286 LOC346887 8 solute carrier family 16 (monocarboxylic acid transporters), member 14 (LOC346887), mRNA. 0.0001256 0.494 211994_at Transcribed locus, Hs.524171 12 strongly similar to XP_508919.1 PREDICTED: similar to protein kinase, lysine deficient 1; kinase deficient protein [Pan troglodytes] 0.0001261 2.214 213836_s_at WD40 repeat protein Hs.463964 WIPI49 17q24.2 Interacting with phosphoInositides of 49 kDa (WIPI49), mRNA. 0.0001271 0.372 212037_at Pinin, desmosome Hs.409965 PNN 14q21.1 associated protein 0.000128 2.586 227384_s_at Similar to KIAA0454 Hs.429365 1q21.1 protein 0.000128 4.614 1553185_at RAS and EF-hand Hs.129136 RASEF 9q21.32 domain containing 0.000129 4.274 231183_s_at jagged 1 (Alagille Hs.224012 JAG1 20p12.1-p11.23 syndrome) (JAG1), mRNA. 0.0001299 0.482 222533_at cereblon (CRBN), Hs.18925 CRBN 3p26.2 mRNA. 0.0001301 2.543 226695_at paired related homeobox Hs.283416 PRRX1 1q24 1 (PRRX1), transcript variant pmx-1b, mRNA. 0.0001301 3.433 217713_x_at ESTs, Weakly similar to ALU6_HUMAN ALU SUBFAMILY SP SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 0.0001306 0.497 225132_at F-box and leucine-rich Hs.508284 FBXL3 13q22 repeat protein 3 (FBXL3), mRNA. 0.0001313 0.484 225179_at Huntingtin interacting Hs.50308 HIP2 4p14 protein 2 0.0001321 3.609 1557432_at RAS protein activator Hs.555904 RASAL2 1q24 like 2 0.0001328 0.224 209612_s_at alcohol dehydrogenase IB Hs.4 ADH1B 4q21-q23 (class I), beta polypeptide (ADH1B), mRNA. 0.0001335 2.071 222753_s_at signal peptidase complex Hs.42194 SPCS3 4q34.2 subunit 3 homolog (S. cerevisiae) (SPCS3), mRNA. 0.0001337 3.162 1555241_at Hypothetical gene Hs.443072 8q21.2 supported by BC055092 0.0001338 0.357 225939_at Eukaryotic translation Hs.476782 EIF4E3 3p14 initiation factor 4E member 3 0.0001341 0.475 217795_s_at transmembrane protein Hs.517817 TMEM43 3p25.1 43 (TMEM43), mRNA. 0.0001341 0.442 200920_s_at B-cell translocation gene Hs.255935 BTG1 12q22 1, anti-proliferative (BTG1), mRNA. 0.0001345 0.108 228202_at Phospholamban Hs.170839 PLN 6q22.1 0.0001347 2.158 220242_x_at zinc finger protein 701 Hs.412951 ZNF701 19q13.41 (ZNF701), mRNA. 0.0001348 0.507 201871_s_at ORF (LOC51035), Hs.351296 LOC51035 11q12.3 mRNA. 0.0001374 3.17 55583_at dedicator of cytokinesis 6 Hs.465918 DOCK6 19p13.2 (DOCK6), mRNA. 0.0001375 2.507 225967_s_at PREDICTED: Hs.356545 LOC284184 17 hypothetical LOC284184 (LOC284184), mRNA. 0.0001389 0.374 218158_s_at adaptor protein Hs.555928 APPL 3p21.1-p14.3 containing pH domain, PTB domain and leucine zipper motif 1 (APPL), mRNA. 0.0001391 2.647 1553569_at Unknown 0.0001405 2.672 232952_at HSPC054 protein Hs.106015 DDEF1 8q24.1-q24.2 0.0001406 3.884 203549_s_at lipoprotein lipase (LPL), Hs.180878 LPL 8p22 mRNA. 0.0001436 0.369 226120_at tetratricopeptide repeat Hs.303055 TTC8 14q31.3 domain 8 (TTC8), transcript variant 3, mRNA. 0.0001439 0.436 222212_s_at LAG1 longevity Hs.285976 LASS2 1q21.2 assurance homolog 2 (S. cerevisiae) (LASS2), transcript variant 3, mRNA. 0.0001441 0.45 224755_at SM-11044 binding Hs.500674 SMBP 10q24.1 protein 0.0001441 0.409 221588_x_at aldehyde dehydrogenase Hs.293970 ALDH6A1 14q24.3 6 family, member A1 (ALDH6A1), nuclear gene encoding mitochondrial protein, mRNA. 0.0001443 0.533 207769_s_at polyglutamine binding protein 1 PQBP1 Xp11.23 (PQBP1), transcript variant 5, mRNA. 0.0001456 0.496 226336_at Peptidylprolyl isomerase Hs.356331 PPIA 7p13-p11.2 A (cyclophilin A) 0.0001456 3.669 216187_x_at X-ray repair Hs.549075 XRCC3 14q32.3 complementing defective repair in Chinese hamster cells 3 0.000146 2.047 218113_at transmembrane protein 2 Hs.494146 TMEM2 9q13-q21 (TMEM2), mRNA. 0.0001463 3.512 207598_x_at X-ray repair Hs.129727 XRCC2 7q36.1 complementing defective repair in Chinese hamster cells 2 (XRCC2), mRNA. 0.0001465 4.648 223697_x_at chromosome 9 open Hs.208914 C9orf64 9q21.32 reading frame 64 (C9orf64), mRNA. 0.0001476 2.584 227396_at Homo sapiens, clone Hs.374451 11 IMAGE: 4454331, mRNA 0.0001482 2.94 243915_at ESTs, Weakly similar to 2109260A B cell growth factor [H. sapiens] 0.0001487 2.694 205367_at adaptor protein with Hs.489448 APS 7q22 pleckstrin homology and src homology 2 domains (APS), mRNA. 0.0001491 0.447 229119_s_at Hypothetical protein Hs.462316 TTC19 17p12 LOC125150 0.0001495 0.332 214359_s_at heat shock 90 kDa protein Hs.509736 HSPCB 6p12 1, beta (HSPCB), mRNA. 0.0001503 0.185 205381_at leucine rich repeat containing 17 LRRC17 7q22.1 (LRRC17), transcript variant 1, mRNA. 0.0001503 0.482 213027_at TROVE domain family, Hs.288178 SSA2 1q31 member 2 0.0001511 0.348 224734_at High-mobility group box 1 Hs.434102 HMGB1 13q12 0.0001511 0.474 207974_s_at S-phase kinase-associated Hs.171626 SKP1A 5q31 protein 1A (p19A) (SKP1A), transcript variant 2, mRNA. 0.0001513 4.07 227952_at Full length insert cDNA Hs.355711 4 clone YI46G04 0.0001514 2.32 240795_at CDNA clone Hs.19452 5 IMAGE: 5288566 0.0001521 0.411 229319_at Homo sapiens, clone Hs.33519 6 IMAGE: 4105966, mRNA 0.0001527 2.413 212414_s_at septin 6 (SEPT6), Hs.496666 38601 Xq24 transcript variant II, mRNA. 0.0001535 0.424 201376_s_at heterogeneous nuclear Hs.808 HNRPF 10q11.21-q11.22 ribonucleoprotein F (HNRPF), mRNA. 0.000154 2.059 50376_at zinc finger protein 444 Hs.24545 ZNF444 19q13.43 (ZNF444), mRNA. 0.0001543 3.085 233319_x_at Phosphatase and actin Hs.225641 PHACTR4 1p35.3 regulator 4 0.000155 0.507 221689_s_at Down syndrome critical Hs.408790 DSCR5 21q22.2 region gene 5 (DSCR5), transcript variant 2, mRNA. 0.000156 2.319 229200_at Hypothetical LOC400813 Hs.13742 1q44 0.0001562 4.302 237475_x_at Selenoprotein P, plasma, 1 Hs.275775 SEPP1 5q31 0.0001564 2.541 1560817_at Mov10, Moloney Hs.514941 MOV10 1p13.2 leukemia virus 10, homolog (mouse) 0.0001583 2.899 232406_at Jagged 1 (Alagille Hs.224012 JAG1 20p12.1-p11.23 syndrome) 0.0001589 2.919 1556138_a_at Collagen, type V, alpha 1 Hs.210283 COL5A1 9q34.2-q34.3 0.0001597 0.435 200651_at guanine nucleotide Hs.5662 GNB2L1 5q35.3 binding protein (G protein), beta polypeptide 2-like 1 (GNB2L1), mRNA. 0.0001618 2.498 241809_at Hypothetical protein Hs.193406 LOC284465 1p13.2 LOC284465 0.0001619 0.456 201484_at suppressor of Ty 4 Hs.439481 SUPT4H1 17q21-q23 homolog 1 (S. cerevisiae) (SUPT4H1), mRNA. 0.0001621 0.526 225475_at mesoderm induction early Hs.21757 MIER1 1p31.2 response 1 homolog (Xenopus laevis) (MIER1), mRNA. 0.0001633 0.329 201529_s_at replication protein A1, Hs.461925 RPA1 17p13.3 70 kDa (RPA1), mRNA. 0.0001637 0.403 212199_at Morf4 family associated Hs.518608 MRFAP1L1 4p16.1 protein 1-like 1 (MRFAP1L1), transcript variant 2, mRNA. 0.0001639 0.387 208796_s_at cyclin G1 (CCNG1), Hs.79101 CCNG1 5q32-q34 transcript variant 2, mRNA. 0.0001644 3.72 238183_at ESTs 0.0001644 3.205 228497_at solute carrier family 22 Hs.125482 SLC22A15 1p13.1 (organic cation transporter), member 15 (SLC22A15), mRNA. 0.0001645 2.614 204078_at synaptonemal complex Hs.446459 SC65 17q21.2 protein SC65 (SC65), mRNA. 0.0001649 3.055 239367_at brain-derived Hs.502182 BDNF 11p13 neurotrophic factor (BDNF), transcript variant 6, mRNA. 0.0001678 2.961 227260_at Transcribed locus Hs.537755 1 0.0001721 0.452 200074_s_at ribosomal protein L14 Hs.446522 RPL14 3p22-p21.2 (RPL14), mRNA. 0.0001731 0.346 227529_s_at A kinase (PRKA) anchor Hs.371240 AKAP12 6q24-q25 protein (gravin) 12 0.0001747 0.451 229844_at Transcribed locus Hs.59368 3 0.0001751 2.202 1568954_s_at Unknown 0.0001753 2.848 1555243_x_at Hypothetical gene Hs.443072 8q21.2 supported by BC055092 0.0001794 0.326 218919_at zinc finger, AN1-type Hs.390395 ZFAND1 8q21.13 domain 1 (ZFAND1), mRNA. 0.0001795 0.337 201674_s_at A kinase (PRKA) anchor Hs.463506 AKAP1 17q21-q23 protein 1 (AKAP1), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA. 0.0001802 2.365 202292_x_at lysophospholipase II Hs.533479 LYPLA2 1p36.12-p35.1 (LYPLA2), mRNA. 0.0001807 3.042 230850_at Formin-like 3 Hs.179838 FMNL3 12q13.12 0.0001808 3.249 202016_at mesoderm specific Hs.270978 MEST 7q32 transcript homolog (mouse) (MEST), transcript variant 3, mRNA. 0.0001816 0.269 209305_s_at growth arrest and DNA- Hs.110571 GADD45B 19p13.3 damage-inducible, beta (GADD45B), mRNA. 0.0001825 2.505 238714_at RAB12, member RAS Hs.270074 18p11.22 oncogene family 0.0001828 0.441 225352_at translocation protein 1 Hs.529591 TLOC1 3q26.2 (TLOC1), mRNA. 0.0001833 0.509 235556_at Transcribed locus, Hs.445247 5 weakly similar to NP_703324.1 glutamic acid-rich protein (garp) [Plasmodium falciparum 3D7] 0.0001833 0.505 1555823_at BS 3076 Hs.170421 14 0.000184 0.349 212188_at potassium channel Hs.109438 KCTD12 13q22.3 tetramerisation domain containing 12 (KCTD12), mRNA. 0.000184 2.716 212769_at Transducin-like enhancer Hs.287362 TLE3 15q22 of split 3 (E(sp1) homolog, Drosophila) 0.0001862 2.329 219289_at hypothetical protein Hs.313917 FLJ20718 16q12.1 FLJ20718 (FLJ20718) transcript variant 1, mRNA. 0.0001871 2.234 229665_at Hypothetical protein Hs.44402 CSTF3 11p13 LOC283267 0.0001876 15.895 231597_x_at ESTs, Weakly similar to T47135 hypothetical protein DKFZp761L0812.1 [H. sapiens] 0.000189 2.944 1558426_x_at Chromosome 7 open Hs.534807 7 reading frame 19 0.0001908 0.386 244050_at similar to RIKEN Hs.136247 LOC401494 9p21.3 4933428I03 (LOC401494), mRNA. 0.0001916 0.44 218311_at mitogen-activated protein Hs.468239 MAP4K3 2p22.1 kinase kinase kinase kinase 3 (MAP4K3), mRNA. 0.0001922 0.441 218373_at fused toes homolog Hs.380897 FTS 16q12.2 (mouse) (FTS), transcript variant 2, mRNA. 0.0001939 0.429 203166_at craniofacial development Hs.461361 CFDP1 16q22.2-q22.3 protein 1 (CFDP1), mRNA. 0.0001953 3.032 214110_s_at ESTs, Highly similar to A43542 lymphocyte-specific protein 1 [H. sapiens] 0.0001962 2.652 229748_x_at Hypothetical protein Hs.487562 LOC285458 4 LOC285458 0.0001971 3.714 240421_x_at CDNA clone Hs.547654 4 IMAGE: 5268630 0.0001976 4.61 213905_x_at Biglycan Hs.821 BGN Xq28 0.0001992 0.426 224812_at 3-hydroxyisobutyrate Hs.406758 HIBADH 7p15.2 dehydrogenase (HIBADH), mRNA. 0.0001997 0.46 200010_at Ribosomal protein L11 Hs.388664 RPL11 1p36.1-p35 0.0002003 0.474 200022_at ribosomal protein L18 Hs.515517 RPL18 19q13 (RPL18), mRNA. 0.0002005 4.122 216858_x_at 0.0002007 0.421 217773_s_at NADH dehydrogenase Hs.50098 NDUFA4 7p21.3 (ubiquinone) 1 alpha subcomplex, 4, 9 kDa (NDUFA4), nuclear gene encoding mitochondrial protein, mRNA. 0.0002018 2.22 1556835_s_at Transcribed locus Hs.548301 11 0.0002019 9.389 203936_s_at matrix metallopeptidase 9 Hs.297413 MMP9 20q11.2-q13.1 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase) (MMP9), mRNA. 0.0002023 2.731 219279_at dedicator of cytokinesis Hs.46578 DOCK10 2q36.3 10 (DOCK10), mRNA. 0.0002042 0.49 230141_at AT rich interactive Hs.161000 ARID4A 14q23.1 domain 4A (RBP1-like) 0.0002053 0.39 204454_at leucine zipper, down- Hs.45231 LDOC1 Xq27 regulated in cancer 1 (LDOC1), mRNA. 0.0002057 0.112 206211_at selectin E (endothelial Hs.89546 SELE 1q22-q25 adhesion molecule 1) (SELE), mRNA. 0.0002058 2.146 227214_at Golgi associated PDZ Hs.191539 GOPC 6q21 and coiled-coil motif containing 0.000206 0.448 224754_at Sp1 transcription factor Hs.524461 SP1 12q13.1 (SP1), mRNA. 0.0002067 0.353 226873_at Transcribed locus Hs.548339 16 0.0002101 0.306 226688_at chromosome 3 open Hs.55131 C3orf23 3p21.33-p21.32 reading frame 23 (C3orf23), transcript variant 1, mRNA. 0.0002108 0.459 222431_at Spindlin Hs.146804 SPIN 9q22.1-q22.3 0.0002111 0.507 226705_at Fibroblast growth factor Hs.264887 FGFR1 8p11.2-p11.1 receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome) 0.0002121 0.267 202350_s_at matrilin 2 (MATN2), Hs.189445 MATN2 8q22 transcript variant 2, mRNA. 0.0002123 3.369 228331_at Chromosome 11 open Hs.502630 C11orf31 11q12.1 reading frame 31 0.0002151 2.308 226599_at KIAA1727 protein Hs.132629 KIAA1727 4q31.3 (KIAA1727), mRNA. 0.000216 0.472 229431_at regulatory factor X- Hs.24422 RFXAP 13q14 associated protein (RFXAP), mRNA. 0.0002181 2.628 210365_at Runt-related transcription Hs.149261 RUNX1 21q22.3 factor 1 (acute myeloid leukemia 1; aml1 oncogene) 0.0002196 3.303 238584_at IQ motif containing with Hs.129174 IQCA 2q37.2-q37.3 AAA domain 0.0002203 0.512 201960_s_at MYC binding protein 2 Hs.151411 MYCBP2 13q22 (MYCBP2), mRNA. 0.0002206 2.459 236715_x_at uveal autoantigen with Hs.108049 UACA 15q22-q24 coiled-coil domains and ankyrin repeats (UACA), transcript variant 1, mRNA. 0.0002226 3.297 213979_s_at C-terminal binding Hs.208597 CTBP1 4p16 protein 1 (CTBP1), transcript variant 1, mRNA. 0.0002231 0.271 208703_s_at amyloid beta (A4) Hs.370247 APLP2 11q24 precursor-like protein 2 (APLP2), mRNA. 0.0002234 0.507 202536_at chromatin modifying Hs.476930 CHMP2B 3p12.1 protein 2B (CHMP2B), mRNA. 0.0002241 4.333 214715_x_at zinc finger protein 160 Hs.467236 ZNF160 19q13.41 (ZNF160), transcript variant 1, mRNA. 0.0002246 0.401 202364_at MAX interactor 1 Hs.501023 MXI1 10q24-q25 (MXI1), transcript variant 3, mRNA. 0.0002266 2.374 221943_x_at ribosomal protein L38 Hs.380953 RPL38 17q23-q25 (RPL38), mRNA. 0.0002277 0.153 1552767_a_at heparan sulfate 6-O- Hs.385956 HS6ST2 Xq26.2 sulfotransferase 2 (HS6ST2), mRNA. 0.0002281 3.22 241223_x_at ESTs, Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] 0.0002292 0.399 207132_x_at prefoldin 5 (PFDN5), Hs.288856 PFDN5 12q12 transcript variant 1, mRNA. 0.0002299 2.574 218739_at abhydrolase domain Hs.19385 ABHD5 3p21 containing 5 (ABHD5), mRNA. 0.0002299 3.3 217497_at Endothelial cell growth Hs.546251 ECGF1 22q13 factor 1 (platelet-derived) 0.0002316 2.781 218193_s_at golgi transport 1 homolog Hs.62275 GOLT1B 12p12.1 B (S. cerevisiae) (GOLT1B), mRNA. 0.0002317 0.315 209146_at sterol-C4-methyl Hs.105269 SC4MOL 4q32-q34 oxidase-like (SC4MOL), transcript variant 2, mRNA. 0.0002325 3.134 201487_at cathepsin C (CTSC), Hs.128065 CTSC 11q14.1-q14.3 transcript variant 1, mRNA. 0.0002331 3.007 202028_s_at ribosomal protein L38 Hs.380953 RPL38 17q23-q25 (RPL38), mRNA. 0.0002336 3.872 217715_x_at ESTs 0.0002337 2.486 1553570_x_at Unknown 0.0002364 0.558 201178_at F-box protein 7 (FBXO7), FBXO7 22q12-q13 transcript variant 2, mRNA. 0.0002365 6.732 210809_s_at periostin, osteoblast Hs.136348 POSTN 13q13.3 specific factor (POSTN), mRNA. 0.0002372 3.675 226997_at CDNA FLJ10196 fis, Hs.12680 5 clone HEMBA1004776 0.0002389 0.316 226038_at LON peptidase N- Hs.180178 LONRF1 8p23.1 terminal domain and ring finger 1 (LONRF1), mRNA. 0.0002408 2.579 AFFX-BioDn- Unknown 5_at 0.0002413 2.498 206857_s_at FK506 binding protein Hs.306834 FKBP1B 2p23.3 1B, 12.6 kDa (FKBP1B), transcript variant 1, mRNA. 0.0002425 0.201 229339_at Myocardin Hs.462257 MYOCD 17p11.2 0.0002453 3.977 242578_x_at Solute carrier family 22 Hs.242721 SLC22A3 6q26-q27 (extraneuronal monoamine transporter), member 3 0.0002463 2.667 231882_at CDNA FLJ10674 fis, Hs.536634 22 clone NT2RP2006436 0.0002463 2.619 1556185_a_at CDNA clone Hs.287168 7 IMAGE: 5260162 0.0002474 1.938 202573_at casein kinase 1, gamma 2 Hs.181390 CSNK1G2 19p13.3 (CSNK1G2), mRNA. 0.0002491 0.533 57715_at Family with sequence Hs.241545 FAM26B 10pter-q26.12 similarity 26, member B 0.000252 4.351 239806_at Transcribed locus Hs.136017 2 0.0002539 2.067 232145_at hypothetical LOC388969 Hs.516159 LOC388969 2p11.2 (LOC388969), mRNA. 0.0002541 0.522 235570_at CDNA FLJ36544 fis, Hs.101689 3 clone TRACH2006378 0.0002548 0.455 224605_at HCV F-transactivated Hs.173705 LOC401152 4q26 protein 1 (LOC401152), mRNA. 0.000255 3.099 205463_s_at Platelet-derived growth Hs.376032 PDGFA 7p22 factor alpha polypeptide 0.0002565 0.51 209384_at proline synthetase co- Hs.304792 PROSC 8p11.2 transcribed homolog (bacterial) (PROSC), mRNA. 0.0002577 5.738 234753_x_at 0.0002578 0.348 235061_at protein phosphatase 1K Hs.291000 PPM1K 4q22.1 (PP2C domain containing) (PPM1K), mRNA. 0.0002619 0.279 235278_at chromosome 20 open reading C20orf133 20p12.1 frame 133 (C20orf133), transcript variant 2, mRNA. 0.0002624 0.147 218730_s_at osteoglycin Hs.109439 OGN 9q22 (osteoinductive factor, mimecan) (OGN), transcript variant 3, mRNA. 0.000263 0.362 1554464_a_at cartilage associated Hs.517888 CRTAP 3p22.3 protein (CRTAP), mRNA. 0.0002644 0.438 226994_at DnaJ (Hsp40) homolog, Hs.368078 DNAJA2 16q11.1-q11.2 subfamily A, member 2 0.000265 3.356 210679_x_at B-cell CLL/lymphoma 7A BCL7A 12q24.13 0.0002653 0.437 206621_s_at Williams-Beuren Hs.520943 WBSCR1 7q11.23 syndrome chromosome region 1 (WBSCR1), transcript variant 2, mRNA. 0.0002657 0.392 1558487_a_at Transmembrane emp24 Hs.510745 TMED4 7p13 protein transport domain containing 4 0.0002665 2.208 1568619_s_at Hypothetical protein Hs.530899 LOC162073 16p12.3 LOC162073 0.0002666 3.366 229795_at Transcribed locus Hs.48945 12 0.0002674 0.312 200906_s_at palladin (KIAA0992), Hs.151220 KIAA0992 4q32.3 mRNA. 0.0002675 2.764 202581_at heat shock 70 kDa protein Hs.274402 HSPA1B 6p21.3 1B (HSPA1B), mRNA. 0.0002697 0.479 225330_at Insulin-like growth factor Hs.20573 IGF1R 15q26.3 1 receptor 0.0002718 2.171 225480_at chromosome 1 open Hs.532749 C1orf122 1p34.3 reading frame 122 (C1orf122), mRNA. 0.0002728 0.412 227132_at HSPC038 protein Hs.374485 LOC51123 8q22.3 (LOC51123), mRNA. 0.0002731 0.533 200031_s_at ribosomal protein S11 Hs.433529 RPS11 19q13.3 (RPS11), mRNA. 0.0002738 0.328 229994_at MRNA; cDNA Hs.379253 1 DKFZp686J23256 (from clone DKFZp686J23256) 0.0002746 3.124 207730_x_at hypothetical protein FLJ20700 FLJ20700 19p13.3 0.0002751 2.866 235327_x_at UBX domain containing Hs.516018 UBXD4 2p23.3 4 (UBXD4), mRNA. 0.0002768 5.302 212236_x at keratin 17 (KRT17), Hs.2785 KRT17 17q12-q21 mRNA. 0.0002777 1.816 218159_at chromosome 20 open Hs.471975 C20orf116 20p13 reading frame 116 (C20orf116), mRNA. 0.0002779 0.309 202119_s_at copine III (CPNE3), Hs.191219 CPNE3 8q21.3 mRNA. 0.000278 2.474 225636_at signal transducer and Hs.530595 STAT2 12q13.3 activator of transcription 2, 113 kDa (STAT2), mRNA. 0.0002844 3.057 224667_x_at Transcribed locus Hs.558150 0.0002846 2.854 233406_at KIAA0256 gene product Hs.9997 KIAA0256 15q21.1 0.0002862 0.464 225941_at Eukaryotic translation Hs.476782 EIF4E3 3p14 initiation factor 4E member 3 0.0002867 0.43 212368_at PREDICTED: zinc finger Hs.485892 ZNF292 6 protein 292 (ZNF292), mRNA.

Example 5 Array Validation

This example provides further support for the use of the endothelial cell tumor-associated molecules provided in Examples 3 and 4 to identify ovarian tumor endothelial cells.

To substantiate the findings provided by the microarray analysis described in Examples 3 and 4, a series of 17 genes were selected at random spanning a range of fold-changes (3.6 to 155.3; FIG. 2). Of 17 primer sets, 15 yielded specific qRT-PCR products when analyzed using Universal Human Reference RNA (Stratagene, La Jolla, Calif.), with 13 reaching statistical significance in tumor (n=10) and normal (n=5) isolates (p<0.05) including PLXDC1, ARBB2, HES4, PGF, EGFL6, ADAM12, COL5A3, COL18A1, PCOLCE, PMAIP1, CENTA2, TMEPAI, and NPTX2. In order to substantiate the pathway analysis (presented below), a second set of genes implicated in endothelial tumor cell signaling was assessed. From a series of 12 genes, suitable primer sets were obtained for 10 genes. All 10 pathway members were successfully validated (p<0.05) including FYN, VAV2, ECGF1, PTK2, TNFAIP6, EZH2, STC1, MMP9, JAG1, and CSPG2 (FIG. 1).

To further examine whether the gene expression alterations identified by the microarray analysis also occur at the protein level, immunohistochemical staining was performed for selected proteins on 5 normal ovaries and 5 invasive epithelial ovarian cancers. The microarray analysis identified FAK (PTK2; 3.1-fold), Fyn (4.7-fold), MMP-9 (9.4-fold), β2-arrestin (4.8-fold), Jagged1 (4.3-fold), and PLXDC1 (10.2-fold) as being significantly increased in tumor-associated endothelial cells, and these changes were validated by real-time RT-PCR.

Immunohistochemical-peroxidase staining confirmed that both FAK and Fyn were indeed overexpressed in the tumor-associated endothelial cells in all samples. There were no obvious differences in protein expression between arterioles and venules. Similarly, increased expression of MMP-9, β2-arrestin, Jagged1, and PLXDC1 was also confirmed at the protein level (FIG. 2). These results provide further support for the use of the specific endothelial cell tumor-associated molecules provided in Examples 3 and 4 to identify ovarian tumor endothelial cells.

Example 6 Modulation of Endothelial Cell Tumor-Associated Molecules

This example illustrates signaling pathways that are modulated in tumor endothelium and their functional significance.

Ovarian epithelial carcinomas arise from molecular events occurring in the epithelial layer, which affect changes in gene expression within surrounding non-epithelial cell populations. For endothelial cells, this altered signaling environment stimulates proliferation, migration, and tumor vascularization. To identify epithelial genes that may be responsible for these changes and the endothelial signaling pathways that are impacted, a series of laser microdissected papillary serous epithelial cell isolates and ovarian surface epithelial brushings were compared, as previously described (Bonome et al., Cancer Res. 65: 10602-10612, 2005). Pathway diagrams were generated using Pathway Assist version 3.0 software. The genes comprising the pathway indicate involvement in endothelial cell proliferation, tube-formation, and cell motility.

To test the biological significance of some of these genes, three genes were selected—EZH2, Jagged1, and PTK2. EZH2 plays an important role in many biological processes and is downstream of Akt activation, making it a potential anti-angiogenic target. siRNA was used to inhibit EZH2 expression (FIG. 3A) in HUVEC cells and its effects on tube formation (FIG. 3D) and migration (FIG. 3E) were examined. In comparison to control non-silencing siRNA, EZH2 silencing resulted in an 85% decrease in endothelial tube-formation on Matrigel (FIG. 3D). EZH2-targeted siRNA completely blocked VEGF-stimulated migration of HUVEC cells (FIG. 3E). Similarly, to determine the functional relevance of Jagged1 for endothelial cell function, the effects of inhibiting Jagged1 expression with siRNA were evaluated (FIG. 3B) on tube-formation (FIG. 3D) and migration (FIG. 3F). Jagged1-targeted siRNA reduced tube-formation by 80% (FIG. 3D) and blocked VEGF-stimulated HUVEC migration (FIG. 3F). Similar results were noted with PTK2 expression inhibition with PTK2-targeted siRNA (FIGS. 3D and 3G). These data indicate that the novel differentially expressed genes in the tumor-associated endothelial cells play functionally significant roles in angiogenesis.

The ability of siRNA to be delivered directly into ovarian tumor cells was investigated by staining tumor tissues with (A) primary rat anti-mouse CD31 antibody to detect endothelial cells and (B) anti-f4/80 to detect scavenging macrophages and then Alexa 488-tagged secondary antibody. Fluorescent siRNA was not only trapped onto blood vessels, but was also effectively delivered deep into tumor parenchyma. Macrophages were observed to surround nests of tumor cells that contained perinuclear siRNA, and had less amount of siRNA compared to tumor cells suggesting that siRNAs were delivered directly into the tumor cells.

The effect of mouse EZH2 siRNA on EZH2-expression in mouse ovarian endothelial cells was also determined. Cells were trypsinized at different time intervals (24 h, 48 h and 72 h) after transfection with mouse EZH2 siRNA and checked for EZH2 mRNA down regulation using RT-PCR analysis. As illustrated in FIG. 4, EZH2 gene expression was significantly decreased after 24 hours of treatment, indicating that the administered siRNA was capable of down-regulating EZH2 mRNA in vitro.

Example 7 Inhibition of Tumor Growth and Vascularization in a Mouse Model

This example describes methods for significantly reducing ovarian tumor growth and vascularization in a mouse model. One of skill in the art will appreciate that similar methods can be used in other mammals and other siRNAs can be used in place of those described herein. Further, a conversion formula known to those of skill in the art can be employed to determine the appropriate doses in other mammals, including humans.

Nude mice were injected (via i.p.) with either 2.5×10⁵ HeyA8 or 1.0×10⁶ SKOV3ip1 cells. Mice were randomly divided into 4 groups: 1) control siRNA-chitosan, 2) mouse EZH2 siRNA-chitosan, 3) Human EZH2 siRNA-chitosan, and 4) combination of mouse plus human EZH2 siRNA-chitosan. Therapy was started on the seventh day by injecting chitosan siRNA twice weekly (150 μg/kg). Therapy was started on the seventh day by injecting chitosan siRNA twice weekly (150 μg/kg) Animals were sacrificed when mice became moribund (3-5 weeks after cell injection). Mouse weight, tumor weight, number of tumor nodules and tumor location were recorded. As illustrated in FIGS. 5 and 6, mice treated with mouse-EZH2 siRNA exhibited significant decrease in tumor burden compared to control siRNA (70% and 42% reduction in tumor weight of HeyA8 and SKOV3ip1 respectively, p=0.05). Human EZH2 siRNA also reduced the tumor burden (50% in HeyA8 and 24% reduction in SKOV3ip1, p=0.05 of only HeyA8 tumors) compared to mouse targeted EZH2 siRNA. However, the greatest reduction was observed when treating the mouse with a combination of mouse plus human EZH2 siRNA (84% and 65% reduction in HeyA8 and SKOV3ip1 tumors, respectively, (p=0.001). In the case of tumor nodules, again combination of mouse plus human EZH2-siRNA group consistently produced fewer tumor nodules with 75% and 53% reduction compared to control group (p=0.05). The effect of EZH2 siRNA on microvessel density was determined by harvesting tumors from the four different groups stated above and staining such tumors for CD31. The mouse targeted EZH2 siRNA group showed decreased number of blood vessels compared to human EZH2 siRNA and control siRNA treated tumors. Microvessel density of the combination treated group using both mouse and human EZH2 siRNA was significantly reduced when compared to that of the control group. These studies demonstrate the ability of EZH2-targeted siRNA to inhibit tumor growth and vascularization in vivo.

Example 8

This example illustrates that increased EZH2 expression in either tumor cells or in tumor vasculature is predictive of poor clinical outcome and that the anti-angiogenesis effect of EZH2 silencing is mediated via silencing VASH1.

Material and Methods.

Human Ovarian Cancer Specimens.

One-hundred and thirty paraffin-embedded epithelial ovarian cancer specimens with available clinical outcome data and confirmed diagnosis by a board-certified gynecologic pathologist were obtained from the Karmanos Cancer Institute tumor bank. All patients were diagnosed from 1985 to 2004 following primary cytoreductive surgery. Slides of tumor samples were obtained for EZH2, CD34, and VEGF expression analysis. Clinical variables obtained for correlative analyses included age at diagnosis, tumor stage and grade, and vital status of patients relative to disease-specific survival at the time of chart review.

Cell Lines and Culture.

The HeyA8 and SKOV3ip1 human epithelial ovarian cancer cells were maintained as described previously. The derivation and characterization of the murine ovarian endothelial cells (MOEC) has been described previously. The EAhy926 endothelial hybridoma cell line was provided by Dr. Robert Danner, CCMD, NIH, and was maintained as described previously, with sodium hypoxanthine and thymidine (HT) supplement (Invitrogen, Carlsbad, Calif.) instead of sodium hypoxanthine aminopterin and thymidine (HAT) supplement (Invitrogen). HUVEC were purchased from Cambrex (Walkersville, Md.) and maintained with heparin and gentamicin/amphotericin-B, as previously described.

EZH2 Promoter Construct.

The EZH2 promoter was amplified by PCR from the Roswell Park Cancer Institute (RPCI) human BAC library 11, Clone-ID RP11-992C19 purchased from the Children's Hospital Oakland Research Institute (Oakland, Calif.), and then cloned into the pGL3-Basic Vector (Promega Corp., Madison, Wis.). The EZH2 promoter construct was amplified using primers (Table 6) with XhoI and HindIII restriction endonuclease sites added to the ends. Purified PCR product was then cloned upstream of the luc+ gene in the pGL3-Basic Vector (Promega Corp.) using XhoI and HindIII.

TABLE 6 Primers and siRNA sequences used. EZH2 promoter (Human): 5′-GATACTCGAGGTCGGGAGTTCGAGACCA-3′ (forward; SEQ ID NO: 6) 5′-GTTTAAGCTTACTCGCGTTGTTCCCGCG-3′ (reverse; SEQ ID NO: 7) VASH1 promoter (Human): 5′-CATGGGAGGGCTTGATGAAGG-3′ (forward; SEQ ID NO: 8) 5′-GCCTAGTCCATGCTGACCTTG-3′ (reverse; SEQ ID NO: 9) Real time quantitative RT-PCR and ChIP assay: Murine EZH2: 5′-GCTGAGCGTATAAAGACACC-3′ (forward; SEQ ID NO: 10) 5′-TCTACATCCTCAGTGGGAAC-3′ (reverse; SEQ ID NO: 11) Human EZH2: 5′-TCATGCAACACCCAACAC-3′ (forward; SEQ ID NO: 12) 5′-CACAACCGGTGTTTCCTC-3′ (reverse; SEQ ID NO: 13) Murine VASH1: 5′-CATCAGGGAGCTGCAGTACA-3′ (forward; SEQ ID NO: 14) 5′-CCCAGCTTCACCTTCTTCAG-3′ (reverse; SEQ ID NO: 15) Human VASH1: 5 -CATGGGAGGGCTTGATGAAGG-3′ (forward; SEQ ID NO: 16) 5′-CAAGGTCAGCATGGACTAGGC-3′ (reverse; SEQ ID NO: 17) Murine E2F1: 5′-TGGATCTGGAGACTGACCAT-3′ (forward; SEQ ID NO: 18) 5′-AGTTGCAGCTGTGTGGTACA-3′ (reverse; SEQ ID NO: 19) Murine E2F2: 5′-GCTCCTGACCAAGAAGTTCA-3′ (forward; SEQ ID NO: 20) 5′-GCAATCACTGTCTGCTCCTT-3′ (reverse; SEQ ID NO: 21) Murine E2F3: 5′-TGCAGTCTGTCTGAGGATGG-3′ (forward; SEQ ID NO: 22) 5′-GAGGCCAGAGGAGAGAGGTT-3′ (reverse; SEQ ID NO: 23) Murine E2F4: 5′-AAGAACTGGACCAGCACAAG-3′ (forward; SEQ ID NO: 24) 5′-ACTATCCAGCAGTGCAGAGG-3′ (reverse; SEQ ID NO: 25) Murine E2F5: 5′-AGTTGTGGCTACAGCAAAGC-3′ (forward; SEQ ID NO: 26) 5′-GGAGAAAGCCGTAAAAGAGG-3′ (reverse; SEQ ID NO: 27) SiRNA target sequences: Nonsilencing control siRNA: 5′-TTCTCCGAACGTGTCACGT[dT][dT]-3′ (Sense; SEQ ID NO: 28) 5′-ACGTGACACGTTCGGAGAA [dT][dT]-3′ (Antisense; SEQ ID NO: 29) Human EZH2 siRNA: Validated sequence Murine EZH2 siRNA1: 5′-GCTCTTACTGCTGAGCGTA[dT][dT]-3′ (Sense; SEQ ID NO: 30) 5′-TACGCTCAGCAGTAAGAGC [dT][dT]-3′ (Antisense; SEQ ID NO: 31) Murine EZH2 siRNA2: 5′-GAGCAAAGCTTGCATTCAT[dT][dT]-3′ (Sense; SEQ ID NO: 32) 5′-ATGAATGCAAGCTTTGCTC [dT][dT]-3′ (Antisense; SEQ ID NO: 33) Murine EZH2 siRNA3: 5′-CATTGGTACTTACTACGAT[dT][dT]-3′ (Sense; SEQ ID NO: 34) 5′-ATCGTAGTAAGTACCAATG [dT][dT]-3′ (Antisense; SEQ ID NO: 35) Human VASH1 siRNA: 5′-GCGATGACTTCCGCAAGGA[dT][dT]-3′ (Sense; SEQ ID NO: 36) 5′-TCCTTGCGGAAGTCATCGC [dT][dT]-3′ (Antisense; SEQ ID NO:37) Murine VASH1 siRNA: 5′-GTGAGCTCGTGCTGGACTA[dT][dT]-3′ (Sense; SEQ ID NO: 38) 5′-TAGTCCAGCACGAGCTCAC [dT][dT]-3′ (Antisense; SEQ ID NO: 39) Murine E2F3 siRNA: 5′-GTTTCTACAGCAAACCTCT[dT][dT]-3′ (Sense; SEQ ID NO: 40) 5′-AGAGGTTTGCTGTAGAAAC [dT][dT]-3′ (Antisense; SEQ ID NO: 41) Murine E2F5 siRNA: 5′-CAATTGCTTTCATGGTGAT[dT][dT]-3′ (Sense; SEQ ID NO: 42) 5′-ATCACCATGAAAGCAATTG [dT][dT]-3′ (Antisense; SEQ ID NO: 43)

Luciferase Reporter Assay.

Relative activity of the EZH2 promoter in the EAhy926 cell line was determined by luciferase reporter assay. Cells were transfected in low-serum medium (0.5% serum) with the firefly luciferase plasmid, either empty vector (pGL3-Basic) or the EZH2 promoter construct vector (EZH2prom-pGL3-Basic), in 12-well plates using Effectene® Transfection Reagent from Qiagen (Valencia, Calif.). The primer sequence of EZH2 promoter are given in Table 6. Cells were then maintained in low-serum medium for 18 hours, washed in warm 1× phosphate-buffered saline (PBS), and treated in triplicate at 37° C. for 6 hours. Treatments included recombinant human (rh) EGF (EGF; 25 ng/mL; Invitrogen) and rhVEGF₁₆₅ (VEGF; 50 ng/mL; Peprotech, Rocky Hill, N.J.), each in fresh medium plus 0.5% serum, fresh complete medium plus 10% serum, and conditioned media from immortalized ovarian surface epithelium (IOSE120) and from papillary serous ovarian cancer cell lines (OVCA420 and SKOV3). Medium in control wells (pGL3-Basic transfectants) was not changed on the day of treatment. Following treatment, cells were washed briefly in cold 1×PBS and lysates were collected and processed using the Dual-Luciferase® Reporter Assay System (Promega Corp.). Firefly luciferase readings were averaged and normalized to pGL3-Basic control readings for percent fold changes.

Chromatin Immunoprecipitation (ChIP) Assay.

HUVEC were cultured in low serum medium (0.5% serum) for 18 h and then treated with or without VEGF (50 ng/mL) for 6 hours. After treatment, ChIP assays were performed using EZ ChIP™ kit (Milllipore, Temecula, Calif.) as described by the manufacturer. Briefly, cross-linked cells were collected, lysed, sonicated and subsequently subjected to immunoprecipitation with EZH2 (Cell signaling) antibody or mouse IgG (mIgG) control. Immunocomplexes were collected with protein G agarose beads and eluted. Cross-links were reversed by incubating at 65° C. DNA then was extracted and purified for PCR using primers (see Table 6) corresponding to the 3800 to 3584 base pairs upstream of the VASH1 transcription start site.

Real Time Quantitative RT-PCR.

Relative expression of EZH2 and VASH1 mRNA in HUVEC and MOEC cells was determined by real-time quantitative RT-PCR. Cells were seeded at 1.0×10⁴ cells per well in 96-well plates in complete medium and incubated at 37° C. for 24 hours, and then in low-serum medium (0.5% serum) for 18 hours, minus EGF and VEGF supplements where appropriate. After washing with warm PBS, cells were treated in triplicate at 37° C. for 6 hours with EGF (25 ng/mL) and VEGF (50 ng/mL), each in fresh medium (lacking supplemental EGF or VEGF) with no serum, fresh complete medium plus 2% serum, and conditioned media. Relative expression of VASH1 mRNA in MOEC cells was determined by transfecting cells with EZH2 mouse siRNA. Samples were collected after 72 hours of transfection. Expression of E2F transcription factors and levels of EZH2 in E2F transcription factors silenced endothelial cells (MOEC) was determined using specific siRNA for E2F transcriptional factors. Real-time quantitative RT-PCR was performed using 50 ng total RNA isolated from treated cells using the RNeasy Mini Kit (Qiagen). (SiRNA and primer sequences are given in Table 6). Relative expression values were obtained using the average of three reference genes and the 2^(−ΔΔCT) method as described previously, and normalized to control for percent fold changes.

SiRNA Constructs and Delivery.

SiRNA nonsilencing control or EZH2 Hs siRNA were purchased from Qiagen and EZH2 Mm siRNA from Dharmacon (Chicago, Ill.). A nonsilencing siRNA that did not share sequence homology with any known human mRNA based on a BLAST search was used as control for target siRNA, and the same sequence with Alexa-555 tag was used to determine the uptake and distribution in tumor and various organs when given in vivo. In vitro transient transfection was performed as described previously and cells were harvested to measure EZH2 protein downregulation by Western blot analysis. (SiRNA sequences are given in Table 6).

DNA Extraction and Methylation Analysis.

DNA was extracted from the EZH2 silencing cells and mock cells using standard phenol-chloroform methods. Methylation analysis was done using a methylation kit (EZ-96 gold; Zymo Research, Orange, Calif.). MethPrimer software was used for the prediction of CpG island of Mm VASH1 (ACCESSION AB284948; VERSION AB284948.1; GI: 118442795) and design of methylation specific primers. The sequence of primers for methylated VASH1 at promoter region was TTAGGGATTTACGTATCGACGT (forward; SEQ ID NO: 44); AAACGACAAACTCCAACCG (reverse; SEQ ID NO: 45); and for unmethlyated VASH1 promoter was TTTTTTTTAGGGATTTATGTATTGATGT (forward; SEQ ID NO: 46); CTAAACAACAAACTCCAACCACA (reverse; SEQ ID NO: 47). The PCR conditions were 94° C. for 5 min with hot start, then 94° C. for 45 second, 56° C. for 45 second, and 72° C. for 45 second, repeated for 40 cycles. Image analysis (Scion Image for Windows) was used for semi-quantitative measurement of methylated and unmethylated VASH1. Methylated VASH1 was normalized by unmethylated VASH1. The studies were repeated 3 times.

Cell Proliferation, Migration and Tube Formation Assay:

Cells were seeded in 96-well plates at 1×10³ cells/well in replicates of 12. After 48 hours, cell growth was arrested; 36 hours after growth arrest, the specific mediators were added to untreated cells. Proliferation is assessed by the MTT dye technique, as previously described. The Membrane Invasion Culture System (MICS) chamber was used to measure the in vitro migration ability of cells.

Orthotopic In Vivo Model of Ovarian Cancer and Tissue Processing.

Female athymic nude mice (NCr-nu) were purchased from the National Cancer Institute-Frederick Cancer Research and Development Center (Frederick, Md.) and maintained as previously described. Tissue specimens were fixed either with formalin or OCT (optimum cutting temperature; Miles, Inc., Elkhart, Ind.) or were snap frozen.

To assess tumor growth for long-term therapy experiments, treatment began 1 week after intraperitoneal injection of tumor cells. Mice were divided into 4 groups (n=10 mice per group): (a) control siRNA/CH, (b) EZH2 Hs siRNA/CH (c) EZH2 Mm siRNA/CH, and (d) EZH2 Hs siRNA/CH plus EZH2 Mm siRNA/CH. VASH1 gene silencing effects was determined using same cells and mice were divided into 6 groups. (a) Control siRNA/CH, (b) EZH2 Mm siRNA 1/CH (c) EZH2 Mm siRNA2/CH, (d) EZH2 Mm siRNA3/CH (e) VASH1 Mm siRNA/CH and (f) VASH1 Mm siRNA/CH plus EZH2 Mm siRNA/CH. Each siRNA was given twice weekly at a dose of 150 μg/kg body weight. Treatment continued until mice became moribund (typically 4 to 5 weeks following tumor-cell injection) in any group. At the time of sacrifice, mouse weight, tumor weight, number of nodules, and distribution of tumors were recorded. The individuals who performed the necropsies, tumor collections, and tissue processing were blinded to the treatment group assignments.

Immunofluorescence and Confocal Microscopy.

Localization of EZH2 and CD31 was performed using frozen tissue. Tumors collected after 48 hours of single injection of control siRNA/CH, or EZH2 Hs siRNA/CH, or EZH2 Mm siRNA/CH, or EZH2 Hs siRNA/CH plus EZH2 Mm siRNA/CH and stained for CD31 and EZH2. Staining for CD31 and desmin was done as described previously. Pericyte coverage was determined by the percent of vessels with 50% or more coverage by the green fluorescence of associated desmin-positive cells in 5 random fields at ×200 magnification for each tumor.

Western Blot Analysis.

Western blot analysis for EZH2 expression, histone3 (Lys27) methylation in vitro and EZH2 expression for in vivo samples was performed as previously reported. Tumors were collected at various time points (after 24, 48, 72 and 96 hours of single injection of control siRNA/CH, or EZH2 Hs siRNA/CH, or EZH2 Mm siRNA/CH, or EZH2 Hs siRNA/CH plus EZH2 Mm siRNA/CH) and lysed to analyze protein levels using Western blotting.

EZH2 Gene Silencing in MOEC.

Relative expression of EZH2 mRNA in MOEC was determined by transfecting cells with control or EZH2 Mm siRNA and harvested after 72 hours of transfection. Real-time quantitative RT-PCR was performed using 50 ng total RNA isolated from treated cells using the RNeasy Mini Kit (Qiagen). Primer sequences are given in the Table 7. Relative expression values were obtained using the average of 3 reference genes and the 2^(−ΔΔCT) method as described previously, and normalized to control for percent fold changes.

TABLE 7 Characteristics of tumors after treatment with EZH2 siRNA/CH and VASH1 siRNA/CH. Median no. nodules p-value Cell line Treatment (range) (vs. control) HeyA8 Control siRNA/CH 19.0 (9-25) EZH2 Mm siRNA1/CH 2.0 (0-8) 0.01* EZH2 Mm siRNA2/CH  9.0 (0-11) 0.046* EZH2 Mm siRNA3/CH  9.0 (2-19) ns VASH1 Mm siRNA/CH  16.0 (12-21) 0.01** EZH2 Mm siRNA1/CH plus 20.0 (7-32) 0.02** VASH1 Mm siRNA/CH *vs control siRNA/CH; **vs EZH2siRNA/CH

Immunohistochemical Staining.

Detection of microvessel density was performed using formalin-fixed, paraffin-embedded tumor sections (8 μm thickness) as previously described. To quantify MVD, the number of blood vessels staining positive for CD31 was recorded in 10 random 0.159 mm² fields at ×200 magnification. All staining was quantified by 2 investigators in a blinded fashion. Immunohistochemistry for EZH2 (1:400 dilution, Zymed, San Francisco, Calif.), CD34 (1:20 dilution, BioGenex Laboratories, San Ramon, Calif.), VEGF (1:100 dilution, Santa Cruz Biotechnology, Inc., Santa Cruz, Calif.) was performed, as described previously. A combined score that was based on the staining intensity and the percentage of cells stained was used to assign a final score.

Statistical Analysis.

Differences in continuous variables such as mean body weight, tumor weight, and proliferation (PCNA) were analyzed using the Mann-Whitney rank sum test. Statistical analyses were performed using SPSS 12.0 for Windows® (SPSS Inc., Chicago, Ill.). A 2-tailed p<0.05 was considered statistically significant. Kaplan-Meier survival plots were generated and comparisons between survival curves were made using the log-rank statistic.

Conditioned Media.

Conditioned media were obtained as follows: IOSE120, OVCA420 and SKOV3 cells were grown in 100 mm culture dishes at 37° C. until 80% confluent. Cells were then washed briefly in warm 1×PBS. Then, 5 mL of low-serum, complete HUVEC cell medium (0.5% serum) was added to the dishes and the cells were incubated at 37° C. for 16 hours. Supernatants (conditioned media) were then collected in a syringe and passed through a 0.45 micron filter and stored at −80° C. until needed.

Preparation of siRNA-Incorporated CH (siRNA/CH) Nanoparticles.

CH (molecular weight 50-190 kDa), sodium tripolyphosphate (TPP), and agarose were purchased from Sigma Co. (St. Louis, Mo.). SiRNA/CH nanoparticles were prepared based on ionic gelation of anionic TPP and siRNA with cationic CH. The formulation of the siRNA/CH nanoparticles is shown in FIG. 11A. Briefly, various concentrations of CH solution was obtained by dissolving CH in 0.25% acetic acid and nanoparticles were spontaneously generated by the addition of TPP (0.25% w/v) and siRNA (1 μg/μL) to CH solution under constant stirring at room temperature. After incubating at 4° C. for 40 min, siRNA/CH nanoparticles were collected by centrifugation (Thermo Biofuge, Germany) at 12,000 rpm for 40 minutes at 4° C. The pellet was washed 3 times to remove unbound chemicals or siRNA and siRNA/CH nanoparticles were stored at 4° C. until used.

Characteristics of siRNA/CH Nanoparticles.

The size and zeta potential of the siRNA/CH nanoparticles were measured by light scattering with a particle size analyzer and Zeta Plus (size and zeta potential analyzer, Brookhaven Instrument Co., CA), respectively. To measure the loading efficiency of siRNA into CH nanoparticles, Alexa-555 fluorescent-labeled siRNA was incorporated into CH nanoparticles followed by centrifugation at 12,000 rpm for 40 minutes. The fluorescence intensity in the supernatant was measured at 590 nm using fluorescence spectrophotometer (Fluostar Optima, BMG Labtech Inc., Durham, N.C.). Additionally, the morphology of CH nanoparticles was confirmed by AFM.

Gel Retardation Assay.

The incorporation of siRNA into CH nanoparticles was determined by 4% agarose gel electrophoresis. Electrophoresis was carried out at a constant voltage of 100 V for 1 hour in 0.5% TAE buffer containing 0.5 μg/mL ethidium bromide (EtBr). The siRNA bands were then visualized under a UV transilluminator (Fluor Chem 8900, Alpha Innotech, Madison, Wis.).

Stability Assay.

Stability of the siRNA-CH nanoparticles in 50% serum was characterized using 4% agarose gel electrophoresis. Either naked siRNA or siRNA/CH nanoparticles were mixed in a 1:1 ratio with fresh serum to get the 50% concentration and incubated at 37° C. Aliquots of 20 μL were collected at selected time intervals, loaded onto an agarose gel followed by electrophoresis to visualize intact siRNA.

Results EZH2 Expression in Human Ovarian Carcinoma

The clinical significance of EZH2 was evaluated in 130 epithelial ovarian cancers. Increased tumoral EZH2 (EZH2-T) expression was noted in 66% of samples and increased expression in the vasculature (EZH2-Endo) was noted in 67% of the samples (FIG. 7A). Increased expression of EZH2-T and EZH2-Endo was significantly associated with high-stage (p values<0.001) and high-grade (p values<0.05; see Table 8) disease. Increased EZH2-T was significantly associated with decreased overall survival (median 2.5 years vs. 7.33 years, p values<0.001; FIG. 7B). Similarly, EZH2-Endo was predictive of poor overall survival (2.33 vs. 8.33 years, p<0.001; FIGS. 7C and 7D). On the basis of pathway-analysis predictions from the disclosed genomic profiling data comparing endothelial cells from epithelial ovarian cancer with those from normal ovarian tissues, the potential associations between EZH2 expression, VEGF expression and microvessel density (MVD) was examined. Increased VEGF expression was strongly associated with increased EZH2-Endo expression (p<0.001; FIGS. 7E and 7F). Moreover, increased EZH2-Endo expression was significantly associated with high MVD counts in the tumor (p<0.001; FIGS. 7G and 7H).

TABLE 8 Association of clinical and demographic features with EZH2 in epithelial ovarian carcinoma. EZH2-T overexpression EZH2-Endo overexpression No Yes p-value No Yes p-value Mean age 59.8 yrs (range 37-89 yrs) Stage Low (I/II) 20 9 <0.001 20 9 <0.001 High (III-IV) 41 108 <0.001 37 112 <0.001 Grade Low 9 7 0.048 10 6 0.005 High 52 112 0.048 37 112 0.005 Histology Serous 22 18 0.002 22 1 <0.001 Others 39 100 0.002 35 104 <0.001

VEGF Increases EZH2 Levels in Endothelial Cells

EAhy926 hybridoma endothelial cells were co-transfected with the Renilla luciferase plasmid and firefly luciferase plasmid either with or without the EZH2 promoter construct. Cells were then treated with VEGF, EGF, or conditioned media from ovarian cancer cell lines. EZH2 promoter activity was determined by the dual-luciferase assay. There was a significant increase in EZH2 promoter activity in endothelial cells in response to VEGF, EGF, and conditioned media (FIG. 8A). In order to examine changes in EZH2 message, HUVECs were treated as indicated above and expression of EZH2 mRNA was examined using quantitative real time RT-PCR. Control values were normalized using 3 housekeeping genes. EZH2 mRNA expression levels were induced (by 130-240% fold change compared to control) in endothelial cells in response to VEGF, EGF, or the conditioned media (FIG. 8B). To examine the relationship between EZH2 and VEGF in human samples, the expression levels of both genes in 29 microdissected high-grade, serous papillary ovarian cancers were determined. Pearson's analysis showed a significant correlation between EZH2 and VEGF levels (p=0.03; FIG. 8C).

EZH2 Silencing Increases VASH1 in Endothelial Cells

To determine the mechanism by which EZH2 silencing could induce anti-angiogenic effects, a whole genome ChIP-on-ChIP analysis was performed. The findings indicate that an anti-angiogenic gene, vasohibin (VASH1) directly binds to EZH2. To validate this finding, a ChIP assay of EZH2 for the VASH1 promoter in endothelial cells in the presence or absence of VEGF was performed (FIG. 9A), which confirmed direct EZH2 binding to the VASH1 promoter. Next, we silenced the EZH2 gene in mouse ovarian endothelial cells (MOEC) using siRNA (FIG. 9B), which resulted in a 2.8 fold increase in VASH1 (FIG. 9C).

To determine the mechanism by which EZH2 regulates VASH1, methylation specific PCR was performed for detecting VASH1 methylation in endothelial cells in the presence of VEGF after silencing EZH2. VEGF treatment resulted in a 1.7 fold increase in VASH1 methlyation compared to the controls. However, EZH2 silencing resulted in a 3.3 fold decrease in VASH1 methylation in the VEGF-treated MOEC cells (FIG. 9D). Specifically, EZH2 gene silencing by decreased histone 3 methlyation at lysine 27 by 2.5 fold in endothelial cells (FIG. 9E).

E2F Mediated Regulation of EZH2 in Endothelial Cells.

The effect of VEGF on E2F1-5 in MOEC is provided in FIG. 10A. There was a significant increase in E2F1, E2F3 and E2F5 following treatment with VEGF (FIG. 10B). To determine which E2F transcription factors might be responsible for increasing EZH2 levels, the effects of VEGF after silencing either E2F1, 3 or 5 were determined. EZH2 levels were significantly decreased in E2F3 and E2F5 silenced cells (FIG. 10B). To validate the binding of EZH2 promoter to E2F3 and E2F5 transcription factors, ChIP assays of EZH2 to these transcription factors were performed. E2F3 and E2F5 were bound to the EZH2 promoters, demonstrating that EZH2 is the direct target of the E2F transcription factors. The studies provide direct explanation for the anti-angiogenesis effects observed in response to EZH2 gene silencing.

VASH1 Gene Silencing Increases the Migration, Tube Formation In Vitro and the Tumor Growth In Vivo

To determine the role of VASH1 on angiogenesis, migration and tube formation studies were performed in MOEC and HUVEC by silencing the VASH1 gene in MOEC and HUVEC. MOEC cells were transfected with control and VASH1 siRNA for 48 hours and then resuspended in serum free media. 75,000 cells were plated on pre-gelatin and Matrigel coated Transwell inserts which were placed in the lower chamber of VEGF containing media. Migration and tube formation were significantly increased after VASH1 gene silencing (FIG. 10C); whereas no change in proliferation of cells.

Whether EZH2 silencing in vivo would affect tumor growth and angiogenesis was determined. Before conducting the EZH2 targeted in vivo experiments, CH nanoparticles for systemic delivery of siRNA into both tumor cells and tumor-associated vasculature were developed and characterize. Several formulations of CH with siRNA (siRNA/CH) were tested (FIG. 11A) and optimized (FIGS. 11B-11E; FIGS. 12A-12B; FIGS. 10A-10C) and the 3:1 ratio (CH:TPP) nanoparticles showed the greatest (75%) incorporation efficiency (FIG. 11B). Therefore, for all subsequent studies, siRNA/CH₃ nanoparticles were used due to their small size, slight positive charge, and high incorporation efficiency of siRNA.

Prior to performing proof-of-concept in vivo efficacy studies, the efficiency of siRNA delivery into orthotopic ovarian tumors was tested. Non-silencing siRNA labeled with Alexa-555 was incorporated into CH nanoparticles and injected intravenously (i.v.) into mice bearing HeyA8 orthotopic tumors (17 days after intraperitoneal inoculation of tumor cells). Tumors were harvested at 15 hours and 3, 5 and 7 days (3 mice per time point) following injection and examined for extent of siRNA delivery. At all time points, punctated emissions of the siRNA were noted in the perinuclear regions of individual cells. SiRNA was noted in >80% of fields examined following a single intravenous injection. To confirm delivery of siRNA in the vasculature, slides were also stained for CD31. siRNA was delivered into the tumor-associated endothelial cells, suggesting potential applications for targeting the tumor vasculature. To confirm intracellular delivery of siRNA, 3-dimensional reconstructions of the tumors using confocal microscopy were created. Lateral views of the optical sections clearly demonstrated the presence of siRNA within the tumor cells (FIGS. 13A and 13B). However, very little siRNA was taken up by macrophages as determined by labeling tissues with f4/80. To examine the delivery of siRNA into other organs, sections of liver, lung, kidney, heart, spleen and brain were also examined, and siRNA delivery was detected in most of these organs.

To examine the in vivo effects of EZH2 gene silencing on tumor growth, EZH2 siRNA directed to either the human (tumor cells; EZH2 Hs siRNA/CH) or mouse (endothelial cells; EZH2 Mm siRNA/CH) sequence were utilized. The specificity of siRNA was confirmed by testing each siRNA in both mouse endothelial (MOEC) and human tumor (HeyA8) cells (FIG. 14). Following intravenous injection of either control siRNA/CH, EZH2 Hs siRNA/CH, EZH2 Mm siRNA/CH, or the combination of EZH2 targeted siRNAs into HeyA8 tumor-bearing mice (n=3 mice per group at each time point), tumors were harvested at different time points and examined for EZH2 protein levels. EZH2 levels were decreased by 24 hours following single injection of EZH2 Hs siRNA/CH with return of expression to baseline expression levels after 96 hours (FIG. 13C). To determine the localization of EZH2 silencing following siRNA/CH administration, we performed dual immunofluorescence staining for EZH2 and CD31. This study further demonstrated that EZH2 Hs siRNA/CH resulted in EZH2 silencing in the tumor cells whereas EZH2 Mm siRNA/CH silenced EZH2 only in the tumor endothelial cells (FIG. 13D).

To determine the therapeutic efficacy of EZH2 gene silencing, a well-characterized orthotopic model of ovarian carcinoma was utilized. Seven days following injection tumor cells into the peritoneal cavity, mice were randomly allocated to 1 of 4 groups of 10 mice each: 1) control siRNA/CH, 2) EZH2 Hs siRNA/CH, 3) EZH2 Mm siRNA/CH and 4) combination of EZH2 Hs siRNA/CH plus EZH2 Mm siRNA/CH. Mice were sacrificed when animals appeared moribund due to significant tumor burden (4 to 5 weeks after cell injection depending on the cell line).

Alexa-555 siRNA uptake into macrophages and to various organs was evaluated. Tumor tissues were collected after single injection of untagged control siRNA/CH or Alexa-555 siRNA/CH nanoparticles and stained with anti-f4/80 antibody to detect scavenging macrophages (green; middle or right panels). Macrophages were seen surrounding nests of tumor cells and had minimal siRNA uptake. Left panel demonstrates lack of natural autofluorescence following injection of untagged control siRNA/CH. Images were taken at original magnification ×200 (left and middle) and ×400 (right). Histological sections were made from the liver, kidney, lung, brain, and heart tissues that were collected after intravenous injection of 5 μg Alexa-555 siRNA/CH nanoparticles and exposed to hematoxylin and eosin (H&E) and Hoechst staining. Left panel represents H&E staining, middle panel represents natural auto-fluorescence of each tissue after a single injection of untagged control siRNA/CH and right panel denotes Alexa-555 siRNA/CH (red). All images were taken at original magnification ×200.

As shown in FIG. 13E and FIG. 15, treatment with EZH2 Mm siRNA/CH resulted in a significant decrease in tumor burden compared to control siRNA/CH (62% reduction in HeyA8; p<0.02 and 40% reduction in SKOV3ip1, p<0.03). EZH2 Hs siRNA/CH as a single-agent had modest effects on tumor growth (p<0.04 for HeyA8; and p<0.05 for SKOV3ip1) compared with control siRNA/CH. However, the greatest reduction was observed with the combination of EZH2 Hs siRNA/CH plus EZH2 Mm siRNA/CH (83% reduction in HeyA8, p<0.001 and 65% reduction in SKOV3ip1, p<0.001). To test for potential off-target effects, we tested the efficacy of 3 additional mouse EZH2 siRNA sequences with similar effects on tumor growth.

To evaluate the effects of EZH2 on other parameters of tumor growth, we examined tumor incidence and number of nodules (Table 9 below). The combination of EZH2 Hs siRNA/CH plus EZH2 Mm siRNA/CH resulted in a significant reduction in tumor nodules in both HeyA8 (p=0.002 vs. control siRNA treated group) and SKOV3ip1 tumors (p=0.004 vs. control siRNA treated group). The decrease in tumor burden occurred despite having comparable tumor incidence. The mean mouse body weight was similar among the different groups, suggesting that feeding and drinking habits were not affected.

TABLE 9 Characteristics of tumors after treatment with human and mouse EZH2 siRNA/CH Median no. nodules p-value Cell line Treatment (range) (vs. control) HeyA8 Control siRNA/CH  6.5 (3-11) EZH2 Hs siRNA/CH  3.5 (1-11) 0.05 EZH2 Mm siRNA/CH 3.0 (1-9) 0.05 EZH2 Hs siRNA/CH plus 1.5 (1-7) 0.002 EZH2 Mm siRNA/CH SKOV3iP1 Control siRNA/CH  16.0 (11-26) EZH2 Hs siRNA/CH 16.0 (8-27) ns EZH2 Mm siRNA/CH 12.0 (1-17) 0.05 EZH2 Hs siRNA/CH plus  7.5 (2-27) 0.004 EZH2 Mm siRNA/CH

Effect of EZH2 Targeting on Tumor Vasculature and Proliferation

To determine the potential mechanisms underlying the efficacy of EZH2 silencing on ovarian tumors, its effects on several biological end points were examined, including MVD, pericyte coverage (desmin) and cell proliferation (PCNA). EZH2 Mm siRNA/CH and the combination therapy groups had significantly lower microvessel density (FIG. 16A) compared to the EZH2 Hs siRNA/CH and control siRNA/CH treated tumors. Pericyte coverage was increased in EZH2 Mm siRNA/CH and the combination groups compared to other 2 groups, suggesting greater vascular maturation (FIG. 16A). Combination treatment with EZH2 Hs siRNA/CH and EZH2 Mm siRNA/CH also resulted in a significant reduction in cell proliferation (FIG. 17).

To determine the requirement for VASH1 in mediating the anti-tumor effects of EZH2 silencing, the effects of VASH1 silencing in combination with EZH2 Mm siRNA/CH was determined. The anti-tumor effect of EZH2 silencing in the tumor vasculature was completely reversed by VASH1 silencing (FIG. 16B and see Table 7) suggesting that VASH1 is required for mediating the anti-tumor effects of EZH2 silencing.

Summary:

The present results provide a new understanding of the regulation of tumor angiogenesis. A novel mechanism by which VEGF increases EZH2 levels in the tumor vasculature was disclosed, which contributes to tumor angiogenesis by inactivating the anti-angiogenic factor, VASH1 via methylation of VASH1 gene and Histone 3 (Lys 27)(H3K27). Moreover, a novel and highly efficient method of gene silencing in the tumor cells as well as in the blood vessels that support their growth was developed and characterized. This approach was highly effective for EZH2 silencing in both compartments.

PcG proteins play a role in determining cell fate during both normal and pathologic processes. Two separate subsets of PcG complexes (PRC1 and PRC2) have been described in humans. PRC1 may be involved in maintenance of repression, whereas PRC2 plays a role in initiating repression. The PRC2 complex includes the EZH2, EED, and SUZ proteins. Altered expression of these proteins has been implicated in cancer pathogenesis. Increased EZH2 levels have been related to cancer cell proliferation and invasion. However, prior to the disclosed work, the role of EZH2 in angiogenesis was not known.

Angiogenesis is regulated by the balance of various pro-angiogenic stimulators, such as VEGF, and several angiogenesis inhibitors, such as angiostatin, endostatin, and antithrombin. On the basis of findings from genomic profiling of endothelial cells from ovarian cancer versus those from normal ovaries, it was discovered that EZH2 expression is significantly increased in tumor-associated endothelial cells. VEGF is well recognized as a pro-angiogenic factor in ovarian and other cancers. In the current study, it was shown for the first time that VEGF can directly increase EZH2 levels in endothelial cells, which in turn inactivating a potent anti-angiogenic factor, VASH1, via methylating VASH1 gene and H3K27. Silencing EZH2 gene resulted in demethylation of VASH1 gene and H3K27 in endothelial cells, which is consistent with other report indicating EZH2 directly controls DNA methylation of EZH2-targeted genes, concomitant with reducing H3K27. Therefore, through this study, a novel mechanism by which tumor angiogenesis is regulated was discovered and a rationale for pursuing EZH2 as a therapeutic target was provided.

While a number of attractive targets in tumor and endothelial cells have been identified, many of these are difficult to target with small molecule inhibitors and monoclonal antibodies. Therefore, RNA interference was employed as a means to target EZH2. Due to limited delivery of siRNA into the tumor-associated endothelial cells with this approach, additional nanoparticles were developed that would allow siRNA delivery into both tumor and tumor-associated endothelial cells. Chitosan (CH) is a naturally occurring polysaccharide with low immunogenicity and low toxicity. Here, CH was used because of its advantageous biological properties such as biodegradability, biocompatibility, and slight positive charge. These properties make use of CH for systemic in vivo siRNA delivery highly attractive. Indeed, the disclosed data demonstrate highly efficient delivery of siRNA incorporated into CH nanoparticles into both tumor and tumor-associated endothelial cells. Therefore, the present work provides an attractive method for systemic delivery of siRNA that could be developed for clinical applications.

Molecular and genetic manipulations have identified EZH2 as a key regulator of tumor angiogenesis here, but these effects do not rule out the possibility that EZH2 has oncogenic functions in the tumor cells. For example, EZH2 has been implicated in cellular transformation, proliferation, and avoidance of apoptosis. Such results imply that multiple signaling pathways likely convey the net effects of EZH2 in promoting tumor growth. However, to the extent that targeting tumor endothelial cells provides therapeutic benefit, interfering with EZH2 in the tumor and endothelial cells represents a novel strategy for treatment of ovarian and other cancers.

In summary, these studies illustrate that increased EZH2 expression in either tumor cells or in tumor vasculature is predictive of poor clinical outcome. The increase in endothelial EZH2 is a direct result of VEGF stimulation and indicates the presence of a paracrine circuit that promotes angiogenesis by methylating (histone H3; lysine 27) and silencing VASH1. EZH2 silencing in tumor cells and in the tumor-associated endothelial cells resulted in inhibition of angiogenesis and ovarian cancer growth. The anti-angiogenic effect was mediated by reactivating VASH1. Thus, these data support the potential for targeting EZH2 as a novel therapeutic approach

Example 9 Screening of Agents to Treat an Ovarian Tumor

This example describes methods that can be used to identify agents to treat an ovarian tumor.

According to the teachings herein, one or more agents for the use of treating an ovarian tumor, such as ovarian cancer can be identified by contacting an ovarian tumor endothelial cell with one or more test agents under conditions sufficient for the one or more test agents to alter the activity of at least one ovarian endothelial cell tumor-associated molecule listed in Tables 1, 2, 3, 4 or 5. The method also includes detecting the activity of the at least one ovarian endothelial cell tumor-associated molecule in the presence and absence of the one or more test agents. The activity of the at least one ovarian endothelial cell tumor-associated molecule in the presence of the one or more test agents is then compared to the activity in the absence of such agents to determine if there is differential expression of the at least one ovarian endothelial cell tumor associated molecule. Differential expression of the ovarian endothelial cell tumor-associated molecule indicates that the one or more test agents is of use to treat the ovarian tumor. For example, a test agent that reduces or inhibits the activity or expression of an ovarian endothelial tumor-associated molecule that is upregulated in ovarian tumor endothelial cells indicates that the test agent is of use to treat the ovarian tumor. Differential expression can be detected at the nucleic acid or protein level. An RNA expression product can be detected by a microarray or PCR by methods described above (see, for example, Example 1). A protein expression product can be detected by standard Western blot or immunoassay techniques that are known to one of skill in the art. However, the disclosure is not limited to particular methods of detection.

Example 10 Identification of Ovarian Endothelial Cell Tumor-Associated Molecule Inhibitors to Alter Tumor Growth and/or Vascularization

This example describes methods that can be used to identify ovarian endothelial cell tumor-associated molecule inhibitors that can be used to target specific genes involved in ovarian tumor growth and/or vascularization.

Based upon the teaching disclosed herein, iSynthetic siRNA molecules are generated against selected target genes, such as any of the ovarian endothelial cell tumor-associated up-regulated genes identified in Examples 2 through 5. In an example, the siRNA molecules are obtained from commercial sources. Knockdown efficiency of the siRNA molecules is assessed as indicated in Example 1. In an example, a significant knockdown efficiency is approximately 20%. As provided in Example 1, the effects of target gene siRNA's on tumor growth and vascularization can be determined by evaluating the effect of siRNA treatment on cell migration and tube formation in HUVECs.

In additional examples, cells are treated with two or more siRNAs (that target two or more genes). The IC₅₀ values are compared (between target gene siRNA individually and in combination) to determine whether the knockdown effect on tumor growth and vascularization is cumulative or additive. siRNAs that reduce or decrease by approximately 20% the activity or expression of the targeted ovarian endothelial cell tumor-associated molecule which is upregulated in ovarian endothelial tumor cells are selected for further study.

Example 11 Effectiveness of an Ovarian Tumor Treatment

This example describes methods that can be used to identify effective ovarian tumor treatments.

Based upon the teachings disclosed herein, the effectiveness of an ovarian tumor treatment can be evaluated by determining the effectiveness of an agent for the treatment of an ovarian tumor in a subject with the ovarian tumor. In an example, the method includes detecting expression of an ovarian endothelial cell tumor-associated molecule in a sample from the subject following treatment with the agent. The expression of the ovarian endothelial cell tumor-associated molecule following treatment is compared to a control (a non-cancerous, ovarian endothelial cell). A reduction or inhibition of the expression or biological activity of the ovarian endothelial cell tumor-associated molecule which is upregulated in ovarian endothelial tumor cells following treatment indicates that the agent is effective for the treatment of an ovarian cancer in the subject. Alternatively, an increase in the expression or biological activity of an ovarian endothelial tumor-associated molecule that is downregulated in ovarian endothelial tumor cells following treatment indicates that the agent is effective for the treatment of the ovarian cancer in the subject. In a specific example, the method includes detecting and comparing the protein expression levels of the ovarian endothelial cell tumor-associated molecules. In other examples, the method includes detecting and comparing the mRNA expression levels of the ovarian endothelial cell tumor-associated molecules.

Example 12 Inhibition of Tumor Growth and/or Vascularization

This example describes methods that can be used to significantly reduce ovarian tumor growth, vascularization in a subject with ovarian cancer.

Based upon the teachings disclosed herein, an ovarian tumor, such as ovarian cancer can be treated by administering a therapeutically effective amount of a composition, wherein the composition comprises a specific binding agent that preferentially binds to one or more ovarian endothelial cell tumor-associated molecules provided in Tables 1 through 5, thereby inhibiting tumor growth and/or vascularization.

In an example, a subject who has been diagnosed with ovarian cancer is identified. In some examples, gene expression is screened to determine which genes are to be targeted. Following subject selection, a therapeutic effective dose of the composition including the specific binding agent is administered to the subject. For example, a therapeutic effective dose of a specific binding agent to one or more of the disclosed ovarian endothelial cell tumor-associated molecules is administered to the subject to reduce or inhibit tumor growth and/or vascularization. In an example, the specific binding agent is a siRNA. In another example, the specific binding agent is an antibody. In a further example, the specific binding agent is conjugated to a therapeutic agent such as a cytotoxin, chemotherapeutic reagent, radionucleotide or a combination thereof.

The amount of the composition administered to prevent, reduce, inhibit, and/or treat ovarian cancer or a condition associated with it depends on the subject being treated, the severity of the disorder, and the manner of administration of the therapeutic composition. Ideally, a therapeutically effective amount of an agent is the amount sufficient to prevent, reduce, and/or inhibit, and/or treat the condition (e.g., ovarian cancer) in a subject without causing a substantial cytotoxic effect in the subject.

In one specific example, siRNAs are incorporated into the neutral liposome DOPC and injected intraperitoneal or intravenously at 150 μg/kg twice weekly for 2 to 3 weeks.

In another specific example, naked antibodies are administered at 5 mg per kg every two weeks or 10 mg per kg every two weeks depending upon the stage of the ovarian cancer. In an example, the antibodies are administered continuously. In another example, antibodies or antibody fragments conjugated to cytotoxic agents (immunotoxins) are administered at 50 μg per kg given twice a week for 2 to 3 weeks.

Example 13 Diagnosis of Metastatic Ovarian Cancer

This example describes particular methods that can be used to diagnose or prognose a metastatic ovarian tumor in a subject, such as metastatic ovarian cancer in a human. However, one skilled in the art will appreciate that similar methods can be used. In some examples, such diagnosis is performed before treating the subject (for example as described in Example 11).

Biological samples are obtained from the subject. If blood or a fraction thereof (such as serum) is used 1-100 μl of blood is collected. Serum can either be used directly or fractionated using filter cut-offs to remove high molecular weight proteins. If desired, the serum can be frozen and thawed before use. If a tissue biopsy sample is used, 1-100 μg of tissue is obtained, for example using a fine needle aspirate RNA or protein is isolated from the tissue using routine methods (for example using a commercial kit).

In one example, pro-angiogenic ovarian endothelial cell tumor-associated nucleic acid expression levels, such as nucleic acid expression levels of EZH2, are determined in a tumor sample obtained from the subject by microarray analysis or real-time quantitative PCR. In an example, the disclosed gene profile is utilized. In other examples, the amount of such molecules is determined at the protein level by methods known to those of ordinary skill in the art, such as Western blot or immunoassay techniques. The relative amount of pro-angiogenic ovarian endothelial cell tumor-associated molecules are compared to a reference value, such as a relative amount of such molecules present in a non-tumor sample from, wherein the presence of significantly greater amounts of pro-angiogenic ovarian endothelial cell tumor-associated molecules listed in Tables 1, 2, 4 and 5 (and indicated to be involved in angiogenesis) in the tumor sample as compared to the non-tumor sample (such as an increase of at least 2-fold, at least 3-fold, or at least 5-fold) indicates that the subject has a metastatic ovarian tumor, has an increased likelihood of an ovarian tumor metastasizing, has a poor prognosis, or combinations thereof. In other examples, a decrease in expression of those molecules listed in Table 3 (and involved in angiogenesis) indicates that the subject has a metastatic ovarian tumor, has an increased likelihood of an ovarian tumor metastasizing, has a poor prognosis, or combinations thereof. In some examples, relative amount of pro-angiogenic ovarian endothelial cell tumor-associated proteins and pro-angiogenic ovarian endothelial cell tumor-associated mRNA expression are determined in the same subject using the methods described above.

While this disclosure has been described with an emphasis upon particular embodiments, it will be obvious to those of ordinary skill in the art that variations of the particular embodiments may be used, and it is intended that the disclosure may be practiced otherwise than as specifically described herein. Features, characteristics, compounds, or examples described in conjunction with a particular aspect, embodiment, or example of the invention are to be understood to be applicable to any other aspect, embodiment, or example of the invention. Accordingly, this disclosure includes all modifications encompassed within the spirit and scope of the disclosure as defined by the following claims. We therefore claim as our invention all that comes within the scope and spirit of these claims. 

We claim:
 1. A method of diagnosing an epithelial ovarian tumor with a poor prognosis in a subject, comprising: contacting a sample containing ovarian tissue, ovarian cells or ovarian endothelial cells obtained from the subject with the epithelial ovarian tumor with at least wild-type JAGGED1 nucleic acid molecule or an anti-wild-type JAGGED1 antibody; comparing expression of at least wild-type JAGGED1 detected in the sample obtained from the subject with the epithelial ovarian tumor to a control; and detecting an at least 2-fold increase in expression of wild-type JAGGED1 relative to a control indicates the subject has a poor prognosis, thereby diagnosing the epithelial ovarian tumor in a subject with a poor prognosis.
 2. The method of claim 1, wherein an at least 2-fold increase in expression of wild-type JAGGED1 as compared to the control indicates a stage III or stage IV epithelial ovarian tumor.
 3. The method of claim 1, wherein an at least 2-fold increase in expression of wild-type JAGGED1 as compared to the control indicates a high grade epithelial ovarian tumor.
 4. The method of claim 1, wherein expression of wild-type JAGGED1 is determined by polymerase chain reaction.
 5. The method of claim 1, further comprising treating the subject with the epithelial ovarian tumor with a poor prognosis by administering to the subject an effective amount of at least one specific binding agent, wherein at least one of the at least one specific binding agents preferentially binds to wild-type JAGGED1 and inhibits epithelial ovarian tumor growth in the subject, wherein the specific binding agent that preferentially binds to wild-type JAGGED1 is a wild-type JAGGED1 siRNA.
 6. The method of claim 1, wherein the control is a sample obtained from a subject that has a non-metastatic ovarian tumor.
 7. The method of claim 1, wherein the wild-type JAGGED 1 nucleic acid molecule or an anti-wild-type JAGGED1 antibody is positioned on an addressable array.
 8. The method of claim 1, further comprising contacting a sample containing ovarian tissue, ovarian cells or ovarian endothelial cells obtained from the subject with the epithelial ovarian tumor with wild-type Zeste homologue 2 (EZH2) nucleic acid molecule or an anti-wild-type EZH2 antibody; comparing expression of at least wild-type EZH2 detected in the sample obtained from the subject with the epithelial ovarian tumor to a control; and detecting an at least 2-fold increase in expression of wild-type EZH2 relative to a control indicates the subject has a poor prognosis, thereby diagnosing the epithelial ovarian tumor in a subject with a poor prognosis.
 9. The method of claim 1, further comprising contacting a sample containing ovarian tissue, ovarian cells or ovarian endothelial cells obtained from the subject with the epithelial ovarian tumor with wild-type protein tyrosine kinase 2 (PTK2) nucleic acid molecule or an anti-wild-type PTK2 antibody; comparing expression of at least wild-type PTK2 detected in the sample obtained from the subject with the epithelial ovarian tumor to a control; and detecting an at least 2-fold increase in expression of wild-type PTK2 relative to a control indicates the subject has a poor prognosis, thereby diagnosing the epithelial ovarian tumor in a subject with a poor prognosis.
 10. The method of claim 1, further comprising contacting a sample containing ovarian tissue, ovarian cells or ovarian endothelial cells obtained from the subject with the epithelial ovarian tumor with wild-type Zeste homologue 2 (EZH2) nucleic acid molecule, an anti-wild-type EZH2 antibody, a wild-type protein tyrosine kinase 2 (PTK2) nucleic acid molecule, or an anti-wild type PTK2 antibody; comparing expression of at least wild-type EZH2 and/or wild-type PTK2 detected in the sample obtained from the subject with the epithelial ovarian tumor to a control; and detecting an at least 2-fold increase in expression of wild-type EZH2 and/or wild-type PTK2 relative to a control indicates the subject has a poor prognosis, thereby diagnosing the epithelial ovarian tumor in a subject with a poor prognosis.
 11. The method of claim 5, wherein the at least one specific binding agent further comprises a specific binding agent that preferentially binds to wild-type EZH2 and is a wild-type EZH2 siRNA.
 12. The method of claim 5, wherein the at least one specific binding agent further comprises a specific binding agent that preferentially binds to wild-type PTK2 and is a wild-type PTK2 siRNA.
 13. The method of claim 5, wherein the at least one specific binding agent further comprises a specific binding that preferentially binds to wild-type PTK2 which is a wild-type PTK2 siRNA and/or a specific binding agent that preferentially binds to wild-type EZH2 which is a wild-type EZH2 siRNA. 